format-version: 1.2
data-version: 1.1
date: 13:01:2012 18:00 ! Always GMT (UTC) or British Summer Time
saved-by: Jon Ison
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: 3234  {since=1.1}
! [Term]
! id: EDAM_operation:XXX {since=1.1}
! name: XXX
! namespace: operation
! subset: operations
! def: "XXX." [http://edamontology.org]
! comment: XXX
! synonym: "XXX" EXACT [http://edamontology.org]
! is_a: EDAM_operation:XXX ! XXX



!
! 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











!
! Top-level concepts (sub-ontologies)
!

[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_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:3031 {since=beta13}
name: Core data
namespace: data
subset: data
def: "A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation." [http://edamontology.org]
comment: Core data entities typically have a format and may be identified by an accession number.
is_a: EDAM_data:0006 ! Data








!
! Topic
!

[Term]
id: EDAM_topic:2807
name: Tool topic
namespace: topic
subset: topics
def: "A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:2809
name: Study topic
namespace: topic
subset: topics
def: "A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:3071 {since=beta13}
name: Biological data resources
namespace: topic
subset: topics
! alt_id: EDAM_topic:2808
def: "A topic concerning primarily a specific type of bioinformatics data, typically the broad category of content of a digital archives of biological data, including databanks, databases proper, web portals and other data resources." [http://edamontology.org]
synonym: "Biological databases" EXACT [http://edamontology.org]
synonym: "Biological data resource" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic


[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:2839
name: Molecules
namespace: topic
subset: topics
def: "Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance." [http://edamontology.org]
synonym: "molecular entity" RELATED [CHEBI:23367]
is_obsolete: true !{since=beta12orEarlier}

[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:2225
name: Protein databases
namespace: topic
subset: topics
def: "Topic concerning protein data resources." [http://edamontology.org]
synonym: "Protein data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources
is_a: EDAM_topic:0078 ! Protein analysis


[Term]
id: EDAM_topic:3174 {since=1.1}
name: Metagenomics
namespace: topic
subset: topics
def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org]
synonym: "Environmental genomics" EXACT [http://edamontology.org]
synonym: "Ecogenomics" EXACT [http://edamontology.org]
synonym: "Community genomics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0610 ! Ecoinformatics
is_a: EDAM_topic:0622 ! Genomics


[Term]
id: EDAM_topic:3172 {since=1.1}
name: Metabolomics
namespace: topic
subset: topics
def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:0079
name: Metabolites
namespace: topic
subset: topics
def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org]
comment: This concept excludes macromolecules such as proteins and nucleic acids.
is_a: EDAM_topic:0154 ! Small molecules
is_a: EDAM_topic:3172 ! Metabolomics

[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:3041 {since=beta13}
name: Sequence databases
namespace: topic
subset: topics
def: "Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles." [http://edamontology.org]
synonym: "Sequence data" EXACT [http://edamontology.org]
synonym: "Sequence data resource" EXACT [http://edamontology.org]
synonym: "Sequence data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources
is_a: EDAM_topic:0080 ! Sequence analysis

[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:3038 {since=beta13}
name: Structure databases
namespace: topic
subset: topics
! alt_id: EDAM_topic:3059
def: "Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids." [http://edamontology.org]
synonym: "Structure data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources
is_a: EDAM_topic:0081 ! Structure analysis


[Term]
id: EDAM_topic:0082
name: Structure prediction
namespace: topic
subset: topics
! alt_id: EDAM_topic:0171
def: "Topic concerning the prediction of molecular (secondary or tertiary) structure." [http://edamontology.org]
is_a: EDAM_topic:0081 ! Structure analysis


[Term]
id: EDAM_topic:0083
name: Alignment
namespace: topic
subset: topics
def: "Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0182 ! Sequence alignment
consider: EDAM_topic:0183 ! Structure alignment
consider: EDAM_topic:0184 ! Threading

[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:0200
name: Microarrays
namespace: topic
subset: topics
! alt_id: EDAM_topic:0206
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_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: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:0122
name: Structural genomics
namespace: topic
subset: topics
def: "Informatics reesources concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism." [http://edamontology.org]
xref: BioCatalogue:Structural Genomics
is_a: EDAM_topic:2226 ! Structure determination
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_topic:3173 {since=1.1}
name: Epigenomics
namespace: topic
subset: topics
def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org]
comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.
synonym: "Epigenetics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0622 ! Genomics



[Term]
id: EDAM_topic:3061 {since=beta13}
name: Documentation and help
namespace: topic
subset: topics
def: "Topic concerning documentation and getting help." [http://edamontology.org]
is_a: EDAM_topic:3068 ! Literature and reference



[Term]
id: EDAM_topic:3047 {since=beta13}
name: Molecular biology reference
namespace: topic
subset: topics
def: "Topic concerning general molecular biology information extracted from the literature." [http://edamontology.org]
xref: BioCatalogue: Document Discovery
xref: BioCatalogue: Literature retrieval
is_a: EDAM_topic:0606 ! Literature data resources


[Term]
id: EDAM_topic:0089
name: Ontology
namespace: topic
subset: topics
! alt_id: EDAM_topic:2255
def: "Topic concerning ontologies, controlled vocabularies, structured glossary or other related resource." [http://edamontology.org]
comment: This includes the annotation of entities (typically biological database entries) with concepts from a controlled vocabulary.
synonym: "Ontologies" EXACT [http://edamontology.org]
synonym: "Applied ontology" NARROW [http://edamontology.org]
xref: BioCatalogue:Ontology
xref: BioCatalogue:Ontology Lookup
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification

[Term]
id: EDAM_topic:0090
name: Data search and retrieval
namespace: topic
subset: topics
! alt_id: EDAM_topic:0155
! alt_id: EDAM_topic:2274
! alt_id: EDAM_topic:0165
def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org]
comment: This includes, for example, search, query and retrieval of molecular sequences and associated data.
synonym: "Data retrieval" EXACT [http://edamontology.org]
xref: BioCatalogue:Sequence Retrieval
xref: BioCatalogue:Data Retrieval
xref: BioCatalogue:Identifier Retrieval
xref: BioCatalogue:Image Retrieval
xref: BioCatalogue:Structure Retrieval
is_a: EDAM_topic:0091 ! Data handling

[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:0092
name: Data visualisation
namespace: topic
subset: topics
def: "Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data." [http://edamontology.org]
synonym: "Data rendering and visualisation" EXACT [http://edamontology.org]
synonym: "Data rendering" EXACT [http://edamontology.org]
synonym: "Data plotting" EXACT [http://edamontology.org]
is_a: EDAM_topic:0091 ! Data handling


[Term]
id: EDAM_topic:2258
name: Chemoinformatics
namespace: topic
subset: topics
def: "Topic for the application of information technology to chemistry." [http://edamontology.org]
synonym: "Cheminformatics" EXACT [http://edamontology.org]
synonym: "Chemical informatics" EXACT [http://edamontology.org]
synonym: "Computational chemistry" EXACT [http://edamontology.org]
xref: BioCatalogue:Chemoinformatics
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:2269
name: Biostatistics
namespace: topic
subset: topics
def: "Topic for the application of statistical methods to biological problems." [http://edamontology.org]
synonym: "Biometry" EXACT [http://edamontology.org]
synonym: "Biometrics" EXACT [http://edamontology.org]
synonym: "Biostatistics" EXACT [http://en.wikipedia.org/wiki/Biostatistics]
xref: BioCatalogue:Biostatistics
is_a: EDAM_topic:0091 ! Data handling

[Term]
id: EDAM_topic:3077 {since=beta13}
! alt_id: EDAM_topic:1779
name: Data acquisition and deposition
namespace: topic
subset: topics
def: "Topic concerning the acquisition and deposition of biological data." [http://edamontology.org]
synonym: "Database submission" EXACT [http://edamontology.org]
is_a: EDAM_topic:0091 ! Data handling


[Term]
id: EDAM_topic:0094
name: Nucleic acid thermodynamics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0614
! alt_id: EDAM_topic:0104
def: "Topic concerning the study of the thermodynamic properties of a nucleic acid." [http://edamontology.org]
comment:  This includes the study of thermal and conformational properties including DNA or DNA/RNA denaturation (melting).
synonym: "Nucleic acid physicochemistry" EXACT [http://edamontology.org]
synonym: "Nucleic acid properties" EXACT [http://edamontology.org]
synonym: "Nucleic acid denaturation" EXACT [http://edamontology.org]
synonym: "DNA melting" EXACT [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis



[Term]
id: EDAM_topic:0097
name: Nucleic acid structure analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0699
! alt_id: EDAM_topic:0106
def: "The processing and analysis of nucleic acid (secondary or tertiary) structural data." [http://edamontology.org]
is_a: EDAM_topic:0081 ! Structure analysis
is_a: EDAM_topic:0077 ! Nucleic acid analysis


[Term]
id: EDAM_topic:3039 {since=beta13}
name: Nucleic acid structure
namespace: topic
subset: topics
! alt_id: EDAM_topic:2833
def: "Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation." [http://edamontology.org]
is_a: EDAM_topic:3038 ! Structure databases


[Term]
id: EDAM_topic:0099
name: RNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0653
def: "Topic concerning RNA sequences and structures." [http://edamontology.org]
is_a: EDAM_topic:3042 ! Nucleic acid sequences


[Term]
id: EDAM_topic:0100
name: Nucleic acid restriction
namespace: topic
subset: topics
def: "Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids." [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis
is_a: EDAM_topic:0821 ! Enzymes and reactions


[Term]
id: EDAM_topic:0107
name: Codon usage analysis
namespace: topic
subset: topics
def: "Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on." [http://edamontology.org]
is_a: EDAM_topic:0110 ! Transcription

[Term]
id: EDAM_topic:0109
name: Gene finding
namespace: topic
subset: topics
def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org]
comment: This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
synonym: "Gene prediction" EXACT [http://edamontology.org]
synonym: "Gene discovery" EXACT [http://edamontology.org]
xref: BioCatalogue:Gene Prediction
is_a: EDAM_topic:3073 ! Nucleic acid feature detection

[Term]
id: EDAM_topic:0110
name: Transcription
namespace: topic
subset: topics
def: "Topic concerning the transcription of DNA into mRNA." [http://edamontology.org]
xref: BioCatalogue:Transcription Factors
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_topic:0108
name: Translation
namespace: topic
subset: topics
def: "Topic concerning the translation of mRNA into protein." [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_topic:0111
name: Promoters
namespace: topic
subset: topics
def: "Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins)." [http://edamontology.org]
xref: BioCatalogue:Promoter Prediction
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0749 ! Transcription factors and regulatory sites

[Term]
id: EDAM_topic:0112
name: Nucleic acid folding
namespace: topic
subset: topics
def: "Topic concerning the folding (in 3D space) of nucleic acid molecules." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0173 ! Nucleic acid structure prediction

[Term]
id: EDAM_topic:0114
name: Gene structure and RNA splicing
namespace: topic
subset: topics
! alt_id: EDAM_topic:0750
def: "Topic concerning introns, exons, gene fusion and RNA splicing (post-transcription RNA modification involving the removal of introns and joining of exons)." [http://edamontology.org]
comment: This includes splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.
synonym: "RNA splicing" EXACT [http://edamontology.org]
synonym: "Gene structure" EXACT [http://edamontology.org]
is_a: EDAM_topic:3062 ! Genetic organisation
is_a: EDAM_topic:0747 ! Nucleic acid sites and features



[Term]
id: EDAM_topic:0123
name: Protein properties
namespace: topic
subset: topics
! alt_id: EDAM_topic:0615
def: "Topic for the study of the physical and biochemical properties of peptides and proteins." [http://edamontology.org]
synonym: "Protein physicochemistry" EXACT [http://edamontology.org]
is_a: EDAM_topic:0639 ! Protein sequence analysis


[Term]
id: EDAM_topic:1775
name: Protein function analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:3057
def: "Topic for the study of protein function." [http://edamontology.org]
is_a: EDAM_topic:0078 ! Protein analysis


[Term]
id: EDAM_topic:0128
name: Protein interactions
namespace: topic
subset: topics
! alt_id: EDAM_topic:0587
def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org]
comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
xref: BioCatalogue:Protein Interaction
is_a: EDAM_topic:1775 ! Protein function analysis
is_a: EDAM_topic:2225 ! Protein databases


[Term]
id: EDAM_topic:0130
name: Protein folding and stability
namespace: topic
subset: topics
def: "Topic concerning protein folding (in 3D space) and protein sequence-structure-function relationships, for example the effect of mutation." [http://edamontology.org]
is_a: EDAM_topic:2814 ! Protein structure analysis

[Term]
id: EDAM_topic:2232
name: Lipoproteins
namespace: topic
subset: topics
def: "Topic concerning lipoproteins (protein-lipid assemblies)." [http://edamontology.org]
is_a: EDAM_topic:0635 ! Specific protein resources

[Term]
id: EDAM_topic:0137
name: Protein hydropathy
namespace: topic
subset: topics
def: "Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein." [http://edamontology.org]
is_a: EDAM_topic:0123 ! Protein properties

[Term]
id: EDAM_topic:0140
name: Protein targeting and localization
namespace: topic
subset: topics
! alt_id: EDAM_topic:0588
def: "Topic for the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export." [http://edamontology.org]
is_a: EDAM_topic:2276 ! Protein function prediction
is_a: EDAM_topic:2225 ! Protein databases


[Term]
id: EDAM_topic:0143
name: Protein structure comparison
namespace: topic
subset: topics
def: "Topic concerning the comparison of two or more protein structures." [http://edamontology.org]
comment: Use this concept for methods that are exclusively for protein structure.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0698 ! Protein tertiary structure
consider: EDAM_topic:1770 ! Structure comparison

[Term]
id: EDAM_topic:2280
name: Nucleic acid structure comparison
namespace: topic
subset: topics
def: "Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures." [http://edamontology.org]
comment: Use this concept for methods that are exclusively for nucleic acid structures.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0097 ! Nucleic acid structure analysis
consider: EDAM_topic:1770 ! Structure comparison

[Term]
id: EDAM_topic:0144
name: Protein residue interaction analysis
namespace: topic
subset: topics
def: "The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures." [http://edamontology.org]
synonym: "Protein residue interactions" EXACT [http://edamontology.org]
is_a: EDAM_topic:2814 ! Protein structure analysis



[Term]
id: EDAM_topic:2276
name: Protein function prediction
namespace: topic
subset: topics
def: "Topic concerning the prediction of functional properties of a protein." [http://edamontology.org]
xref: BioCatalogue:Function Prediction
is_a: EDAM_topic:1775 ! Protein function analysis

[Term]
id: EDAM_topic:0147
name: Protein-protein interactions
namespace: topic
subset: topics
! alt_id: EDAM_topic:0719
def: "Topic concerning protein-protein interactions, protein complexes, protein functional coupling etc." [http://edamontology.org]
is_a: EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_topic:0148
name: Protein-ligand interactions
namespace: topic
subset: topics
! alt_id: EDAM_topic:0717
def: "Topic concerning protein-ligand (small molecule) interactions." [http://edamontology.org]
xref: BioCatalogue:Ligand Interaction
is_a: EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_topic:0149
name: Protein-nucleic acid interactions
namespace: topic
subset: topics
! alt_id: EDAM_topic:0718
def: "Topic concerning protein-DNA/RNA interactions." [http://edamontology.org]
is_a: EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_topic:0150
name: Protein design
namespace: topic
subset: topics
def: "Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein." [http://edamontology.org]
is_a: EDAM_topic:0172 ! Protein structure prediction


[Term]
id: EDAM_topic:0151
name: G protein-coupled receptors (GPCR)
namespace: topic
subset: topics
def: "Topic concerning G-protein coupled receptors (GPCRs)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0820 ! Membrane proteins

[Term]
id: EDAM_topic:2278
name: Transmembrane protein prediction
namespace: topic
subset: topics
def: "Predict transmembrane domains and topology in protein sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0820 ! Membrane proteins
consider: EDAM_topic:0178 ! Protein secondary structure prediction

[Term]
id: EDAM_topic:0152
name: Carbohydrates
namespace: topic
subset: topics
! alt_id: EDAM_topic:0695
def: "Topic concerning carbohydrates, typically including structural information." [http://edamontology.org]
is_a: EDAM_topic:3038 ! Structure databases

[Term]
id: EDAM_topic:0153
name: Lipids
namespace: topic
subset: topics
! alt_id: EDAM_topic:2624
def: "Topic concerning lipids and their structures." [http://edamontology.org]
is_a: EDAM_topic:3038 ! Structure databases

[Term]
id: EDAM_topic:0154
name: Small molecules
namespace: topic
subset: topics
! alt_id: EDAM_topic:0696
def: "Topic concerning small molecules of biological significance, typically including structural information." [http://edamontology.org]
comment: Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides.  Structural data is usually included.
synonym: "molecular entity" RELATED [CHEBI:23367]
is_a: EDAM_topic:3038 ! Structure databases



[Term]
id: EDAM_topic:0156
name: Sequence editing
namespace: topic
subset: topics
def: "Edit, convert or otherwise change a molecular sequence, either randomly or specifically." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0080 ! Sequence analysis
consider: EDAM_topic:0091 ! Data handling

[Term]
id: EDAM_topic:0157
name: Sequence composition analysis
namespace: topic
subset: topics
def: "Processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity or repeats." [http://edamontology.org]
is_a: EDAM_topic:0080 ! Sequence analysis





[Term]
id: EDAM_topic:0158
name: Sequence motifs
namespace: topic
subset: topics
! alt_id: EDAM_topic:0161
! alt_id: EDAM_topic:0162
def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org]
synonym: "Motifs" EXACT [http://edamontology.org]
is_a: EDAM_topic:0594 ! Sequence classification


[Term]
id: EDAM_topic:0188
name: Sequence profiles and HMMs
namespace: topic
subset: topics
! alt_id: EDAM_topic:0744
! alt_id: EDAM_topic:0746
! alt_id: EDAM_topic:1763
def: "Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment." [http://edamontology.org]
comment: Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
is_a: EDAM_topic:0594 ! Sequence classification

[Term]
id: EDAM_topic:0159
! alt_id: EDAM_topic:2260
! alt_id: EDAM_topic:2261
name: Sequence comparison
namespace: topic
subset: topics
def: "Topic concerning the comparison of two or more molecular sequences." [http://edamontology.org]
comment: The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
xref: BioCatalogue:Protein Sequence Similarity
xref: BioCatalogue:Nucleotide Sequence Similarity
is_a: EDAM_topic:0080 ! Sequence analysis


[Term]
id: EDAM_topic:0160
name: Sequence sites and features
namespace: topic
subset: topics
! alt_id: EDAM_topic:0600
def: "Topic concerning the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org]
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:3072 {since=beta13}
name: Sequence feature detection
namespace: topic
subset: topics
def: "Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences." [http://edamontology.org]
is_a: EDAM_topic:0080 ! Sequence analysis


[Term]
id: EDAM_topic:0163
name: Sequence database search
namespace: topic
subset: topics
def: "Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [http://edamontology.org]
comment: The query is a sequence-based entity such as another sequence, a motif or profile.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0159 ! Sequence comparison

[Term]
id: EDAM_topic:3052 {since=beta13}
name: Sequence clusters and classification
namespace: topic
subset: topics
def: "Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity." [http://edamontology.org]
comment: This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
synonym: "Sequence clusters" EXACT [http://edamontology.org]
synonym: "Sequence families" EXACT [http://edamontology.org]
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:0164
name: Sequence clustering
namespace: topic
subset: topics
def: "Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities." [http://edamontology.org]
comment: This includes systems that generate, process and analyse sequence clusters.
is_a: EDAM_topic:0159 ! Sequence comparison


[Term]
id: EDAM_topic:0594
name: Sequence classification
namespace: topic
subset: topics
def: "Topic concerning the classification of molecular sequences based on some measure of their similarity." [http://edamontology.org]
comment: Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
is_a: EDAM_topic:0080 ! Sequence analysis




[Term]
id: EDAM_topic:0166
name: Protein structural motifs and surfaces
namespace: topic
subset: topics
! alt_id: EDAM_topic:0139
! alt_id: EDAM_topic:0170
! alt_id: EDAM_topic:0146
! alt_id: EDAM_topic:0589
def: "Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules." [http://edamontology.org]
comment: This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on.
synonym: "Protein structural features" EXACT [http://edamontology.org]
synonym: "Protein surfaces" EXACT [http://edamontology.org]
synonym: "Protein structural motifs" EXACT [http://edamontology.org]
synonym: "Structural motifs" EXACT [http://edamontology.org]
is_a: EDAM_topic:0698 ! Protein tertiary structure

[Term]
id: EDAM_topic:0167
name: Structural (3D) profiles
namespace: topic
subset: topics
! alt_id: EDAM_topic:0599
def: "The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment." [http://edamontology.org]
synonym: "Structural profiles" EXACT [http://edamontology.org]
is_a: EDAM_topic:1770 ! Structure comparison

[Term]
id: EDAM_topic:1770
! alt_id: EDAM_topic:0168
! alt_id: EDAM_topic:0169
name: Structure comparison
namespace: topic
subset: topics
def: "Topic concerning the comparison of two or more molecular structures." [http://edamontology.org]
comment: This might involve comparison of secondary or tertiary (3D) structural information.
is_a: EDAM_topic:0081 ! Structure analysis

[Term]
id: EDAM_topic:2844
name: Structural clustering
namespace: topic
subset: topics
def: "Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters." [http://edamontology.org]
synonym: "Structure classification" EXACT [http://edamontology.org]
is_a: EDAM_topic:1770 ! Structure comparison



[Term]
id: EDAM_topic:2271
name: Structure database search
namespace: topic
subset: topics
def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [http://edamontology.org]
comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:1770 ! Structure comparison


[Term]
id: EDAM_topic:0172
name: Protein structure prediction
namespace: topic
subset: topics
def: "Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features." [http://edamontology.org]
xref: BioCatalogue:Protein Structure Prediction
is_a: EDAM_topic:0082 ! Structure prediction
is_a: EDAM_topic:2814 ! Protein structure analysis

[Term]
id: EDAM_topic:0173
name: Nucleic acid structure prediction
namespace: topic
subset: topics
! alt_id: EDAM_topic:0181
def: "Topic concerning the folding of nucleic acid molecules and particularly the prediction or design of (typically RNA) secondary or tertiary structure." [http://edamontology.org]
synonym: "Nucleic acid folding" EXACT [http://edamontology.org]
synonym: "RNA/DNA structure prediction" EXACT [http://edamontology.org]
xref: BioCatalogue:Nucleotide Structure Prediction
xref: BioCatalogue:Nucleotide Secondary Structure
xref: BioCatalogue:Nucleotide Tertiary Structure
is_a: EDAM_topic:0082 ! Structure prediction
is_a: EDAM_topic:0097 ! Nucleic acid structure analysis

[Term]
id: EDAM_topic:2953
name: Nucleic acid design
namespace: topic
subset: topics
def: "Topic for the design of nucleic acid sequences with specific conformations." [http://edamontology.org]
is_a: EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_topic:0174
name: Ab initio structure prediction
namespace: topic
subset: topics
def: "Topic for the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [http://edamontology.org]
synonym: "de novo protein structure prediction" EXACT [http://edamontology.org]
is_a: EDAM_topic:0082 ! Structure prediction

[Term]
id: EDAM_topic:2275
name: Molecular modelling
namespace: topic
subset: topics
def: "Topic for the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. " [http://edamontology.org]
is_a: EDAM_topic:0082 ! Structure prediction
is_a: EDAM_topic:0172 ! Protein structure prediction

[Term]
id: EDAM_topic:0175
name: Homology modelling
namespace: topic
subset: topics
def: "Topic for the modelling of the three-dimensional structure of a protein using known sequence and structural data." [http://edamontology.org]
synonym: "Comparative modelling" EXACT [http://edamontology.org]
is_a: EDAM_topic:2275 ! Molecular modelling

[Term]
id: EDAM_topic:0176
! alt_id: EDAM_topic:0145
name: Molecular dynamics
namespace: topic
subset: topics
def: "Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org]
comment: This includes resources concerning flexibility and motion in protein and other molecular structures.
synonym: "Molecular motions" EXACT [http://edamontology.org]
synonym: "Molecular flexibility" EXACT [http://edamontology.org]
is_a: EDAM_topic:2275 ! Molecular modelling

[Term]
id: EDAM_topic:0177
name: Molecular docking
namespace: topic
subset: topics
def: "Topic for modelling the structure of proteins in complex with small molecules or other macromolecules." [http://edamontology.org]
is_a: EDAM_topic:2275 ! Molecular modelling

[Term]
id: EDAM_topic:0178
name: Protein secondary structure prediction
namespace: topic
subset: topics
def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org]
xref: BioCatalogue:Protein Secondary Structure
is_a: EDAM_topic:0172 ! Protein structure prediction
is_a: EDAM_topic:0694 ! Protein secondary structure

[Term]
id: EDAM_topic:0179
name: Protein tertiary structure prediction
namespace: topic
subset: topics
def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org]
xref: BioCatalogue:Protein Tertiary Structure
is_a: EDAM_topic:0172 ! Protein structure prediction
is_a: EDAM_topic:0698 ! Protein tertiary structure

[Term]
id: EDAM_topic:0180
name: Protein fold recognition
namespace: topic
subset: topics
def: "Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s)." [http://edamontology.org]
is_a: EDAM_topic:0172 ! Protein structure prediction


[Term]
id: EDAM_topic:0182
name: Sequence alignment
namespace: topic
subset: topics
! alt_id: EDAM_topic:2283
! alt_id: EDAM_topic:0185
! alt_id: EDAM_topic:0186
! alt_id: EDAM_topic:0187
! alt_id: EDAM_topic:0596
! alt_id: EDAM_topic:0189
def: "Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments)." [http://edamontology.org]
comment: This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
xref: BioCatalogue:Protein Sequence Alignment
xref: BioCatalogue:Nucleotide Sequence Alignment
xref: BioCatalogue:Protein Pairwise Alignment
xref: BioCatalogue:Nucleotide Pairwise Alignment
xref: BioCatalogue:Protein Multiple Alignment
xref: BioCatalogue:Nucleotide Multiple Alignment
is_a: EDAM_topic:0159 ! Sequence comparison
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:3178
name: RNA-Seq alignment
namespace: topic
subset: topics
def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome.  This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org]
synonym: "RNA-seq alignment" EXACT [http://edamontology.org]
is_a: EDAM_topic:0182 ! Sequence alignment




[Term]
id: EDAM_topic:0183
! alt_id: EDAM_topic:2272
! alt_id: EDAM_topic:2273
name: Structure alignment
namespace: topic
subset: topics
! alt_id: EDAM_topic:0597
! alt_id: EDAM_topic:0190
def: "Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [http://edamontology.org]
comment: This includes the generation, storage, analysis, rendering etc. of structure alignments.
synonym: "Structure alignment generation" EXACT [http://edamontology.org]
is_a: EDAM_topic:1770 ! Structure comparison
is_a: EDAM_topic:3038 ! Structure databases


[Term]
id: EDAM_topic:0184
name: Threading
namespace: topic
subset: topics
def: "Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [http://edamontology.org]
synonym: "Sequence-structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_topic:0180 ! Protein fold recognition



[Term]
id: EDAM_topic:0191
name: Phylogeny reconstruction
namespace: topic
subset: topics
def: "Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree." [http://edamontology.org]
comment: Currently too specific for the topic sub-ontology (but might be unobsoleted).
xref: BioCatalogue:Tree Inference
xref: BioCatalogue:Evolutionary Distance Measurements
is_a: EDAM_topic:0084 ! Phylogenetics



[Term]
id: EDAM_topic:2257
name: Phylogeny visualisation
namespace: topic
subset: topics
def: "Visualise a phylogeny, for example, render a phylogenetic tree." [http://edamontology.org]
xref: BioCatalogue:Tree Display
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0084 ! Phylogenetics


[Term]
id: EDAM_topic:0194
name: Phylogenomics
namespace: topic
subset: topics
def: "Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction." [http://edamontology.org]
is_a: EDAM_topic:0084 ! Phylogenetics
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_topic:2842
name: High-throughput sequencing
namespace: topic
subset: topics
def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org]
synonym: "Next-generation sequencing" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:3168 ! Sequencing

[Term]
id: EDAM_topic:0195
name: Virtual PCR
namespace: topic
subset: topics
def: "Topic concerning simulated polymerase chain reaction (PCR)." [http://edamontology.org]
synonym: "PCR" EXACT [http://edamontology.org]
synonym: "Polymerase chain reaction" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_topic:0196
name: Sequence assembly
namespace: topic
subset: topics
def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org]
is_a: EDAM_topic:3168 ! Sequencing


[Term]
id: EDAM_topic:0133
name: Two-dimensional gel electrophoresis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0765
def: "Topic concerning two-dimensional gel electrophoresis image and related data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0121 ! Proteomics




[Term]
id: EDAM_topic:0134
name: Mass spectrometry
namespace: topic
subset: topics
! alt_id: EDAM_topic:0766
def: "Topic concerning mass spectrometry and related data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0121 ! Proteomics


[Term]
id: EDAM_topic:0135
name: Protein microarrays
namespace: topic
subset: topics
def: "Topic concerning protein microarray data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0121 ! Proteomics
consider: EDAM_topic:0200 ! Microarrays


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

[Term]
id: EDAM_topic:3168 {since=1.1}
name: Sequencing
namespace: topic
subset: topics
def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis


[Term]
id: EDAM_topic:3169 {since=1.1}
name: ChIP-seq
namespace: topic
subset: topics
def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org]
synonym: "Chip-sequencing" EXACT [http://edamontology.org]
synonym: "Chip sequencing" EXACT [http://edamontology.org]
synonym: "Chip seq" EXACT [http://edamontology.org]
is_a: EDAM_topic:3168 ! Sequencing
is_a: EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_topic:3179 {since=1.1}
name: ChIP-on-chip
namespace: topic
subset: topics
def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org]
synonym: "ChIP-chip" EXACT [http://edamontology.org]
is_a: EDAM_topic:3168 ! Sequencing
is_a: EDAM_topic:0128 ! Protein interactions



[Term]
id: EDAM_topic:3170 {since=1.1}
name: RNA-Seq
namespace: topic
subset: topics
def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.  " [http://edamontology.org]
comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
synonym: "RNA-seq" EXACT [http://edamontology.org]
synonym: "Small RNA-Seq" EXACT [http://edamontology.org]
synonym: "Small RNA-seq" EXACT [http://edamontology.org]
synonym: "Whole transcriptome shotgun sequencing" EXACT [http://edamontology.org]
synonym: "WTSS" EXACT [http://edamontology.org]
is_a: EDAM_topic:3168 ! Sequencing
is_a: EDAM_topic:0203 ! Transcriptomics





[Term]
id: EDAM_topic:3177 {since=1.1}
name: DNA-Seq
namespace: topic
subset: topics
def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org]
synonym: "DNA-seq" EXACT [http://edamontology.org]
is_a: EDAM_topic:3168 ! Sequencing


[Term]
id: EDAM_topic:3062 {since=beta13}
name: Genetic organisation
namespace: topic
subset: topics
def: "Topic concerning the structural and functional organisation of genes and other genetic elements." [http://edamontology.org]
is_a: EDAM_topic:2816 ! Gene resources




[Term]
id: EDAM_topic:0204
name: Gene regulation
namespace: topic
subset: topics
! alt_id: EDAM_topic:3049
! alt_id: EDAM_topic:0631
def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org]
synonym: "Gene regulation resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:2816 ! Gene resources


[Term]
id: EDAM_topic:0199
name: Genetic variation
namespace: topic
subset: topics
! alt_id: EDAM_topic:0626
def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org]
synonym: "Mutation and polymorphism" EXACT [http://edamontology.org]
synonym: "DNA variation" EXACT [http://edamontology.org]
is_a: EDAM_topic:0625 ! Genotype and phenotype
is_a: EDAM_topic:3041 ! Sequence databases
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_topic:0202
name: Pharmacoinformatics
namespace: topic
subset: topics
def: "Topic for the application of information technology to drug research, including the structure, effects of and response to drugs, drug design and so on." [http://edamontology.org]
synonym: "Computational pharmacology" EXACT [http://edamontology.org]
is_a: EDAM_topic:2258 ! Chemoinformatics

[Term]
id: EDAM_topic:0203
name: Transcriptomics
namespace: topic
subset: topics
alt_id: EDAM_topic:0197
def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org]
comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein.
synonym: "Gene expression profiling" EXACT [http://edamontology.org]
synonym: "Expression profiling" EXACT [http://edamontology.org]
synonym: "Gene expression resources" EXACT [http://edamontology.org]
synonym: "Gene expression analysis" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic
is_a: EDAM_topic:2816 ! Gene resources
is_a: EDAM_topic:0203 ! Transcriptomics


[Term]
id: EDAM_topic:2277
name: SNPs
namespace: topic
subset: topics
def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org]
comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.
is_a: EDAM_topic:0199 ! Genetic variation


[Term]
id: EDAM_topic:0208
name: Pharmacogenomics
namespace: topic
subset: topics
def: "Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [http://edamontology.org]
synonym: "Pharmacogenetics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0202 ! Pharmacoinformatics
is_a: EDAM_topic:0622 ! Genomics

[Term]
id: EDAM_topic:0209
name: Drug design
namespace: topic
subset: topics
def: "Topic concerning the design of drugs or potential drug compounds." [http://edamontology.org]
comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
is_a: EDAM_topic:0202 ! Pharmacoinformatics

[Term]
id: EDAM_topic:0210
name: Fish
namespace: topic
subset: topics
def: "Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a fish, a group of fish or all fish.
is_a: EDAM_topic:2820 ! Vertebrates

[Term]
id: EDAM_topic:0211
name: Flies
namespace: topic
subset: topics
def: "Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a fly, a group of flies or all flies.
synonym: "Fly" EXACT [http://edamontology.org]
is_a: EDAM_topic:2819 ! Invertebrates

[Term]
id: EDAM_topic:3048 {since=beta13}
name: Mammals
namespace: topic
subset: topics
def: "Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation." [http://edamontology.org]
is_a: EDAM_topic:2820 ! Vertebrates


[Term]
id: EDAM_topic:0213
name: Mice or rats
namespace: topic
subset: topics
def: "Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a group of mice / rats or all mice / rats.
synonym: "Mouse or rat" EXACT [http://edamontology.org]
is_a: EDAM_topic:3048 ! Mammals



[Term]
id: EDAM_topic:0215
name: Worms
namespace: topic
subset: topics
def: "Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a worm, a group of worms or all worms.
synonym: "Worm" EXACT [http://edamontology.org]
is_a: EDAM_topic:2819 ! Invertebrates


[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:0606
name: Literature data resources
namespace: topic
subset: topics
def: "Data resources for the biological or biomedical literature, either a primary source of literature or some derivative." [http://edamontology.org]
is_a: EDAM_topic:3068 ! Literature and reference
is_a: EDAM_topic:3071 ! Biological data resources


[Term]
id: EDAM_topic:3068 {since=beta13}
name: Literature and reference
namespace: topic
subset: topics
def: "Topic concerning the scientific literature, reference information and documentation." [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:0218
name: Text mining
namespace: topic
subset: topics
def: "Topic concerning the analysis of the biomedical and informatics literature." [http://edamontology.org]
synonym: "Text data mining" EXACT [http://edamontology.org]
xref: BioCatalogue:Text Mining
xref: BioCatalogue:Document Similarity
xref: BioCatalogue:Document Clustering
xref: BioCatalogue:Named Entity Recognition
is_a: EDAM_topic:0217 ! Literature analysis


[Term]
id: EDAM_topic:0219
name: Annotation
namespace: topic
subset: topics
! alt_id: EDAM_topic:2256
def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org]
synonym: "Ontology annotation" EXACT [http://edamontology.org]
xref: BioCatalogue:Genome Annotation
xref: BioCatalogue:Ontology Annotation
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification

[Term]
id: EDAM_topic:0221
name: Sequence annotation
namespace: topic
subset: topics
def: "Annotate a molecular sequence." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0219 ! Annotation


[Term]
id: EDAM_topic:0222
name: Genome annotation
namespace: topic
subset: topics
def: "Annotate a genome." [http://edamontology.org]
xref: BioCatalogue:Genome Annotation
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0219 ! Annotation
consider: EDAM_topic:0621 ! Genome, proteome and model organisms



[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_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:2811
name: Nomenclature
namespace: topic
subset: topics
! alt_id: EDAM_topic:0619
def: "Topic concerning biological nomenclature (naming), symbols and terminology." [http://edamontology.org]
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification

[Term]
id: EDAM_topic:2229
name: Cell biology resources
namespace: topic
subset: topics
def: "Topic concerning cells, such as key genes and proteins involved in the cell cycle." [http://edamontology.org]
is_a: EDAM_topic:3070 ! Biological science resources


[Term]
id: EDAM_topic:3064 {since=beta13}
name: Developmental biology resources
namespace: topic
subset: topics
def: "Topic concerning how organisms grow and develop." [http://edamontology.org]
is_a: EDAM_topic:3070 ! Biological science resources

[Term]
id: EDAM_topic:3067 {since=beta13}
name: Anatomy resources
namespace: topic
subset: topics
def: "Topic concerning the structures of living organisms." [http://edamontology.org]
is_a: EDAM_topic:3070 ! Biological science resources




[Term]
id: EDAM_topic:3065 {since=beta13}
name: Embryology resources
namespace: topic
subset: topics
def: "Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage." [http://edamontology.org]
is_a: EDAM_topic:3064 ! Developmental biology resources


[Term]
id: EDAM_topic:3053 {since=beta13}
name: Genetics
namespace: topic
subset: topics
! alt_id: EDAM_topic:2227
def: "Topic concerning the study of genes, genetic variation and heredity in living organisms." [http://edamontology.org]
synonym: "Genetics data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:2226
name: Structure determination
namespace: topic
subset: topics
! alt_id: EDAM_topic:0136
def: "Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, including the assignment or modelling of molecular structure from such data." [http://edamontology.org]
synonym: "Structural determination" EXACT [http://edamontology.org]
synonym: "Structural assignment" EXACT [http://edamontology.org]
synonym: "Structure assignment" EXACT [http://edamontology.org]
synonym: "Raw structural data analysis" EXACT [http://edamontology.org]
is_a: EDAM_topic:0081 ! Structure analysis



[Term]
id: EDAM_topic:0595
name: Protein classification
namespace: topic
subset: topics
! alt_id: EDAM_topic:0129
def: "Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc." [http://edamontology.org]
is_a: EDAM_topic:0078 ! Protein analysis
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification
is_a: EDAM_topic:0594 ! Sequence classification

[Term]
id: EDAM_topic:0598
name: Sequence motif or profile
namespace: topic
subset: topics
def: "Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type." [http://edamontology.org]
comment: This includes comparison, discovery, recognition etc. of sequence motifs.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0158 ! Sequence motifs
consider: EDAM_topic:0188 ! Sequence profiles and HMMs


[Term]
id: EDAM_topic:0601
name: Protein modifications
namespace: topic
subset: topics
! alt_id: EDAM_topic:0142
def: "Topic concerning protein chemical modifications, e.g. post-translational modifications." [http://edamontology.org]
comment: EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)
synonym: "Protein post-translation modification" EXACT [http:edamontology.souceforge.net]
synonym: "protein modification" RELATED [MOD:00000]
synonym: "protein modification process" RELATED [GO:0006464]
is_a: EDAM_topic:0123 ! Protein properties
is_a: EDAM_topic:2225 ! Protein databases

[Term]
id: EDAM_topic:0602
name: Pathways, networks and models
namespace: topic
subset: topics
alt_id: EDAM_topic:3076 {since=beta13}
! alt_id: EDAM_topic:0198
! alt_id: EDAM_topic:0755
def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org]
synonym: "Network or pathway analysis" EXACT [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:3075 {since=beta13}
name: Biological system modelling
namespace: topic
subset: topics
def: "Topic for modelling biological systems in mathematical terms." [http://edamontology.org]
xref: BioCatalogue:Model Analysis
xref: BioCatalogue:Model Execution
is_a: EDAM_topic:2259 ! Systems biology



[Term]
id: EDAM_topic:2259
name: Systems biology
namespace: topic
subset: topics
def: "Topic concerning the holistic modelling and analysis of biological systems and the interactions therein." [http://edamontology.org]
synonym: "Systems biology" EXACT [http://en.wikipedia.org/wiki/Systems_biology]
xref: BioCatalogue:Systems Biology
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_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:0608
name: Cell culture resources
namespace: topic
subset: topics
def: "Topic concerning general cell culture or data on a specific cell lines." [http://edamontology.org]
is_a: EDAM_topic:0607 ! Laboratory resources


[Term]
id: EDAM_topic:0610
name: Ecoinformatics
namespace: topic
subset: topics
def: "Topic concerning the application of information technology to the ecological and environmental sciences." [http://edamontology.org]
synonym: "Computational ecology" EXACT [http://edamontology.org]
synonym: "Ecological informatics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:3063 {since=beta13}
name: Medical informatics resources
namespace: topic
subset: topics
! alt_id: EDAM_topic:0087
def: "Topic for the application of information technology to health, disease and biomedicine." [http://edamontology.org]
synonym: "Health and disease" EXACT [http://edamontology.org]
synonym: "Healthcare informatics" EXACT [http://edamontology.org]
synonym: "Health informatics" EXACT [http://edamontology.org]
synonym: "Clinical informatics" EXACT [http://edamontology.org]
synonym: "Biomedical informatics" EXACT [http://edamontology.org]
is_a: EDAM_topic:0607 ! Laboratory resources


[Term]
id: EDAM_topic:3050 {since=beta13}
name: Biodiversity
namespace: topic
subset: topics
def: "Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet." [http://edamontology.org]
synonym: "Biodiversity data resource" EXACT [http://edamontology.org]
synonym: "Biodiversity data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:0610 ! Ecoinformatics


[Term]
id: EDAM_topic:2840
name: Toxicoinformatics
namespace: topic
subset: topics
def: "Topic concerning the adverse effects of chemical substances on living organisms." [http://edamontology.org]
synonym: "Computational toxicology" EXACT [http://edamontology.org]
is_a: EDAM_topic:2258 ! Chemoinformatics

[Term]
id: EDAM_topic:2661
name: Toxins and targets
namespace: topic
subset: topics
def: "Topic concerning structural and associated data for toxic chemical substances." [http://edamontology.org]
is_a: EDAM_topic:2840 ! Toxicoinformatics
is_a: EDAM_topic:0154 ! Small molecules

[Term]
id: EDAM_topic:0611
name: Electron microscopy
namespace: topic
subset: topics
def: "Topic concerning electron microscopy data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:2226 ! Structure determination

[Term]
id: EDAM_topic:2828
name: X-ray crystallography
namespace: topic
subset: topics
def: "Topic concerning X-ray crystallography data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:2226 ! Structure determination

[Term]
id: EDAM_topic:0593
name: NMR
namespace: topic
subset: topics
def: "Topic concerning raw NMR data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:2226 ! Structure determination



[Term]
id: EDAM_topic:0612
name: Cell cycle
namespace: topic
subset: topics
! alt_id: EDAM_topic:0609
def: "Topic concerning the cell cycle including key genes and proteins." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:2229 ! Cell biology resources


[Term]
id: EDAM_topic:0613
name: Peptides and amino acids
namespace: topic
subset: topics
! alt_id: EDAM_topic:0604
def: "Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides." [http://edamontology.org]
is_a: EDAM_topic:0154 ! Small molecules


[Term]
id: EDAM_topic:0616
name: Organelle genes and proteins
namespace: topic
subset: topics
def: "Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome)." [http://edamontology.org]
is_a: EDAM_topic:3078 ! Gene and protein resources

[Term]
id: EDAM_topic:0617
name: Ribosomal genes and proteins
namespace: topic
subset: topics
def: "Topic concerning ribosomes, typically of ribosome-related genes and proteins." [http://edamontology.org]
synonym: "Ribosome genes and proteins" EXACT [http://edamontology.org]
is_a: EDAM_topic:0616 ! Organelle genes and proteins


[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

[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: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] born obsolete
! id: EDAM_topic:3054 {since=beta13}
! name: Molecular genetics
! namespace: topic
! subset: topics
! def: "Topic concerning the structure and function of genes at a molecular level." [http://edamontology.org]
! is_obsolete: true !{since=beta13}
! consider: EDAM_topic:3053 ! Genetics


[Term]
id: EDAM_topic:3055 {since=beta13}
name: Quantitative genetics
namespace: topic
subset: topics
def: "Topic concerning the genes, Mendelian inheritance and mechanisms underlying continuous phenotypic traits (such as height or weight)." [http://edamontology.org]
is_a: EDAM_topic:3053 ! Genetics


[Term]
id: EDAM_topic:3056 {since=beta13}
name: Population genetics
namespace: topic
subset: topics
def: "Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow." [http://edamontology.org]
is_a: EDAM_topic:3053 ! Genetics




[Term]
id: EDAM_topic:0623
name: Genes, gene family or system
namespace: topic
subset: topics
def: "Topic concerning particular gene(s), gene system or groups of genes." [http://edamontology.org]
is_a: EDAM_topic:3052 ! Sequence clusters and classification
is_a: EDAM_topic:2816 ! Gene resources



[Term]
id: EDAM_topic:0624
name: Chromosomes
namespace: topic
subset: topics
def: "Topic concerning chromosomes." [http://edamontology.org]
is_a: EDAM_topic:3062 ! Genetic organisation

[Term]
id: EDAM_topic:3175 {since=1.1}
name: Structural variation
namespace: topic
subset: topics
def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org]
synonym: "Genomic structural variation" EXACT [http://edamontology.org]
is_a: EDAM_topic:0624 ! Chromosomes
is_a: EDAM_topic:0199 ! Genetic variation




[Term]
id: EDAM_topic:0625
name: Genotype and phenotype
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]
synonym: "Genotyping" EXACT [http://edamontology.org]
synonym: "Genotype and phenotype resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:2816 ! Gene resources

[Term]
id: EDAM_topic:3078 {since=beta13}
name: Gene and protein resources
namespace: topic
subset: topics
def: "Topic concerning specific genes and their encoded proteins or a related group of such genes and proteins." [http://edamontology.org]
synonym: "Genes and proteins resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:0635 ! Specific protein resources
is_a: EDAM_topic:0623 ! Genes, gene family or system


[Term]
id: EDAM_topic:3070 {since=beta13}
name: Biological science resources
namespace: topic
subset: topics
! alt_id: EDAM_topic:3066
def: "Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org]
synonym: "Phenotype resource" EXACT [http://edamontology.org]
is_a: EDAM_topic:3071 ! Biological data resources


[Term]
id: EDAM_topic:0629
name: Gene expression and microarray
namespace: topic
subset: topics
def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0203 ! Transcriptomics
consider: EDAM_topic:0200 ! Microarrays


[Term]
id: EDAM_topic:0634
name: Disease resources
namespace: topic
subset: topics
def: "Topic concerning diseases." [http://edamontology.org]
is_a: EDAM_topic:0625 ! Genotype and phenotype

[Term]
id: EDAM_topic:2813
name: Disease genes and proteins
namespace: topic
subset: topics
! alt_id: EDAM_topic:0819
def: "Topic concerning the genes, gene variations and proteins involved in one or more specific diseases." [http://edamontology.org]
is_a: EDAM_topic:0634 ! Disease resources
is_a: EDAM_topic:3078 ! Gene and protein resources

[Term]
id: EDAM_topic:0635
name: Specific protein resources
namespace: topic
subset: topics
def: "Topic concerning a particular protein, protein family or other group of proteins." [http://edamontology.org]
synonym: "Specific protein" EXACT [http://edamontology.org]
is_a: EDAM_topic:2225 ! Protein databases


[Term]
id: EDAM_topic:0637
name: Taxonomy
namespace: topic
subset: topics
def: "Topic concerning organism classification, identification and naming." [http://edamontology.org]
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification


[Term]
id: EDAM_topic:0639
name: Protein sequence analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0125
def: "Processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org]
xref: BioCatalogue:Protein Sequence Analysis
is_a: EDAM_topic:0080 ! Sequence analysis
is_a: EDAM_topic:0078 ! Protein analysis

[Term]
id: EDAM_topic:3043 {since=beta13}
name: Protein sequences
namespace: topic
subset: topics
def: "Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org]
xref: BioCatalogue:Protein Sequence Analysis
is_a: EDAM_topic:3041 ! Sequence databases
is_a: EDAM_topic:2225 ! Protein databases

[Term]
id: EDAM_topic:0640
name: Nucleic acid sequence analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0096
def: "Processing and analysis of nucleotide sequences and sequence-based entities such as alignments, motifs and profiles." [http://edamontology.org]
xref: BioCatalogue:Nucleotide Sequence Analysis
is_a: EDAM_topic:0080 ! Sequence analysis
is_a: EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_topic:3042 {since=beta13}
name: Nucleic acid sequences
namespace: topic
subset: topics
def: "Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles." [http://edamontology.org]
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:0641
name: Repeat sequences
namespace: topic
subset: topics
! alt_id: EDAM_topic:2262
def: "Topic concerning the repetitive nature of molecular sequences." [http://edamontology.org]
synonym: "Repeat sequence" EXACT [http://edamontology.org]
xref: BioCatalogue:Repeats
is_a: EDAM_topic:0157 ! Sequence composition analysis
is_a: EDAM_topic:3041 ! Sequence databases

[Term]
id: EDAM_topic:0642
name: Low complexity sequences
namespace: topic
subset: topics
! alt_id: EDAM_topic:2263
def: "Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity." [http://edamontology.org]
is_a: EDAM_topic:0157 ! Sequence composition analysis
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:0644
name: Proteome
namespace: topic
subset: topics
def: "Topic concerning a specific proteome including protein sequences and annotation." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0080 ! Sequence analysis

! [Term]
! id: EDAM:0000646
! name: BLAST
! namespace: resources
! def: "A BLAST-format database of sequences." [http://edamontology.org]
! is_obsolete: true !{since=beta12orEarlier}
! consider: EDAM_topic:3041 ! Sequence database



[Term]
id: EDAM_topic:0654
name: DNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0098
! alt_id: EDAM_topic:0666
! alt_id: EDAM_topic:0627
! alt_id: EDAM_topic:0628
def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org]
comment: The DNA sequences might be coding or non-coding sequences.
synonym: "DNA analysis" EXACT [http://edamontology.org]
is_a: EDAM_topic:3042 ! Nucleic acid sequences
is_a: EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_topic:3176
name: DNA packaging
namespace: topic
subset: topics
def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org]
is_a: EDAM_topic:0654 ! DNA
is_a: EDAM_topic:0624 ! Chromosomes


[Term]
id: EDAM_topic:3171 {since=1.1}
name: DNA methylation
namespace: topic
subset: topics
def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org]
is_a: EDAM_topic:0654 ! DNA




[Term]
id: EDAM_topic:0655
name: mRNA, EST or cDNA database
namespace: topic
subset: topics
! alt_id: EDAM_topic:0205
def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org]
synonym: "Transcriptome" EXACT [http://edamontology.org]
synonym: "Transcriptome database" EXACT [http://edamontology.org]
synonym: "mRNA, EST or cDNA" EXACT [http://edamontology.org]
is_a: EDAM_topic:0099 ! RNA

[Term]
id: EDAM_topic:0659
name: Functional and non-coding RNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0113
! alt_id: EDAM_topic:0119
! alt_id: EDAM_topic:0664
! alt_id: EDAM_topic:0665
! alt_id: EDAM_topic:0120
def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org]
comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA).
synonym: "Non-coding RNA" EXACT [http://edamontology.org]
synonym: "Functional RNA" EXACT [http://edamontology.org]
is_a: EDAM_topic:0099 ! RNA


[Term]
id: EDAM_topic:3060 {since=beta13}
name: Regulatory RNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0661
! alt_id: EDAM_topic:0662
! alt_id: EDAM_topic:0117
! alt_id: EDAM_topic:0118
def: "Topic concerning regulatory RNA sequences including  microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org]
comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression.
is_a: EDAM_topic:0659 ! Functional and non-coding RNA


[Term]
id: EDAM_topic:0660
name: rRNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0116
def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org]
is_a: EDAM_topic:0659 ! Functional and non-coding RNA


[Term]
id: EDAM_topic:0663
name: tRNA
namespace: topic
subset: topics
! alt_id: EDAM_topic:0115
def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org]
is_a: EDAM_topic:0659 ! Functional and non-coding RNA


[Term]
id: EDAM_topic:2814
name: Protein structure analysis
namespace: topic
subset: topics
! alt_id: EDAM_topic:0126
! alt_id: EDAM_topic:0590
alt_id: EDAM_topic:3040 {since=beta13}
def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org]
synonym: "Protein structure" EXACT [http://edamontology.org]
is_a: EDAM_topic:0078 ! Protein analysis
is_a: EDAM_topic:0081 ! Structure analysis
is_a: EDAM_topic:3038 ! Structure databases
is_a: EDAM_topic:2225 ! Protein databases


[Term]
id: EDAM_topic:0694
name: Protein secondary structure
namespace: topic
subset: topics
! alt_id: EDAM_topic:2124
def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org]
comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
synonym: "Protein secondary structure analysis" EXACT [http://edamontology.org]
is_a: EDAM_topic:2814 ! Protein structure analysis

[Term]
id: EDAM_topic:0698
name: Protein tertiary structure
namespace: topic
subset: topics
! alt_id: EDAM_topic:2125
def: "Topic concerning protein tertiary structures." [http://edamontology.org]
synonym: "Protein tertiary structure analysis" EXACT [http://edamontology.org]
is_a: EDAM_topic:2814 ! Protein structure analysis




[Term]
id: EDAM_topic:0697
name: RNA structure and alignment
namespace: topic
subset: topics
def: "Topic concerning RNA secondary or tertiary structure and alignments." [http://edamontology.org]
synonym: "RNA structure" EXACT [http://edamontology.org]
synonym: "RNA structure alignment" EXACT [http://edamontology.org]
synonym: "RNA alignment" EXACT [http://edamontology.org]
is_a: EDAM_topic:0183 ! Structure alignment

[Term]
id: EDAM_topic:2826
name: Protein structure alignment
namespace: topic
subset: topics
def: "Topic concerning protein secondary or tertiary structure alignments." [http://edamontology.org]
is_a: EDAM_topic:0183 ! Structure alignment
is_a: EDAM_topic:2814 ! Protein structure analysis


[Term]
id: EDAM_topic:0620
name: Drugs and targets
namespace: topic
subset: topics
def: "Topic concerning the structures of drugs, drug target, their interactions and binding affinities." [http://edamontology.org]
is_a: EDAM_topic:0154 ! Small molecules
is_a: EDAM_topic:0202 ! Pharmacoinformatics

[Term]
id: EDAM_topic:0618
name: Scents
namespace: topic
subset: topics
def: "A database about scents." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0154 ! Small molecules



[Term]
id: EDAM_topic:0722
name: Nucleic acid classification
namespace: topic
subset: topics
def: "Topic concerning nucleic acid classification (typically sequence classification)." [http://edamontology.org]
is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification
is_a: EDAM_topic:0077 ! Nucleic acid analysis
is_a: EDAM_topic:0594 ! Sequence classification

! [Term]
! id: EDAM:0000723
! name: Protein structure classification
! namespace: resources
! def: "Topic concerning protein structural classifications." [http://edamontology.org]
! is_obsolete: true !{since=beta12orEarlier}
! consider: EDAM_topic:1770 ! Structure comparison
! consider: EDAM_topic:0736 ! Protein domains and folds


[Term]
id: EDAM_topic:0724
name: Protein families
namespace: topic
subset: topics
def: "Topic concerning primarily proteins that have been classified as members of a protein family (or other grouping)." [http://edamontology.org]
comment: A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
synonym: "Protein sequence classification" EXACT [http://edamontology.org]
synonym: "Protein secondary" EXACT [http://edamontology.org]
is_a: EDAM_topic:3052 ! Sequence clusters and classification
is_a: EDAM_topic:2225 ! Protein databases

[Term]
id: EDAM_topic:0736
name: Protein domains and folds
namespace: topic
subset: topics
! alt_id: EDAM_topic:0703
! alt_id: EDAM_topic:0700
! alt_id: EDAM_topic:0127
def: "Topic concerning protein tertiary structural domains and folds." [http://edamontology.org]
xref: BioCatalogue:Domains
is_a: EDAM_topic:0698 ! Protein tertiary structure
is_a: EDAM_topic:0724 ! Protein families


[Term]
id: EDAM_topic:0740
name: Nucleic acid sequence alignment
namespace: topic
subset: topics
def: "Topic concerning nucleotide sequence alignments." [http://edamontology.org]
is_a: EDAM_topic:0182 ! Sequence alignment
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_topic:0741
name: Protein sequence alignment
namespace: topic
subset: topics
def: "Topic concerning protein sequence alignments." [http://edamontology.org]
comment: A sequence profile typically represents a sequence alignment.
is_a: EDAM_topic:0182 ! Sequence alignment
is_a: EDAM_topic:0639 ! Protein sequence analysis

! [Term]
! id: EDAM:0000742
! name: Sequence motif or profile (nucleotide)
! namespace: resources
! def: "Topic concerning nucleotide sequence motifs, or sequence profiles derived from an nucleic acid sequence alignment." [http://edamontology.org]
! is_obsolete: true !{since=beta12orEarlier}
! consider: EDAM_topic:0158 ! Sequence motifs


! [Term]
! id: EDAM:0000743
! name: Sequence motif or profile (protein)
! namespace: resources
! def: "Topic concerning protein sequence motifs, or sequence profiles derived from an protein sequence alignment." [http://edamontology.org]
! is_obsolete: true !{since=beta12orEarlier}
! consider: EDAM_topic:0158 ! Sequence motifs



[Term]
id: EDAM_topic:0747
name: Nucleic acid sites and features
namespace: topic
subset: topics
! alt_id: EDAM_topic:0105
! alt_id: EDAM_topic:0095
def: "Topic concerning positional features such as functional sites in nucleotide sequences." [http://edamontology.org]
synonym: "Nucleic acid functional sites" EXACT [http://edamontology.org]
synonym: "Nucleic acid features" EXACT [http://edamontology.org]
is_a: EDAM_topic:0160 ! Sequence sites and features
is_a: EDAM_topic:3042 ! Nucleic acid sequences


[Term]
id: EDAM_topic:3073 {since=beta13}
name: Nucleic acid feature detection
namespace: topic
subset: topics
def: "Topic concerning the detection of positional features such as functional sites in nucleotide sequences." [http://edamontology.org]
is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis
is_a: EDAM_topic:3072 ! Sequence feature detection


[Term]
id: EDAM_topic:0748
name: Protein sites and features
namespace: topic
subset: topics
! alt_id: EDAM_topic:0124
! alt_id: EDAM_topic:0138
def: "Topic concerning positional features such as functional sites in protein sequences." [http://edamontology.org]
synonym: "Protein functional sites" EXACT [http://edamontology.org]
synonym: "Protein sequence features" EXACT [http://edamontology.org]
is_a: EDAM_topic:0160 ! Sequence sites and features
is_a: EDAM_topic:3043 ! Protein sequences


[Term]
id: EDAM_topic:3074 {since=beta13}
name: Protein feature detection
namespace: topic
subset: topics
def: "Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites." [http://edamontology.org]
is_a: EDAM_topic:0639 ! Protein sequence analysis
is_a: EDAM_topic:3072 ! Sequence feature detection


[Term]
id: EDAM_topic:0749
name: Transcription factors and regulatory sites
namespace: topic
subset: topics
! alt_id: EDAM_topic:0811
def: "Topic concerning transcription factors; proteins that bind to DNA and control transcription of DNA to mRNA, either promoting (as an activator) or blocking (as a repressor) the binding to DNA of RNA polymerase, and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences." [http://edamontology.org]
comment: This includes promoters, enhancers, silencers and boundary elements / insulators.  This includes sequence and structural information, binding profiles etc, and may also include the transcription factor binding site in DNA.
synonym: "Transcriptional regulatory sites" EXACT [http://edamontology.org]
synonym: "Transcription factors" EXACT [http://edamontology.org]
synonym: "Transcription factor and binding site" EXACT [http://edamontology.org]
is_a: EDAM_topic:0204 ! Gene regulation
is_a: EDAM_topic:0110 ! Transcription
is_a: EDAM_topic:0635 ! Specific protein resources
is_a: EDAM_topic:0747 ! Nucleic acid sites and features
is_a: EDAM_topic:3062 ! Genetic organisation
is_a: EDAM_topic:3073 ! Nucleic acid feature detection



[Term]
id: EDAM_topic:0751
name: Phosphorylation sites
namespace: topic
subset: topics
def: "Topic concerning protein phosphorylation and phosphorylation sites in protein sequences." [http://edamontology.org]
! is_a: EDAM_topic:0601 ! Protein modifications
! is_a: EDAM_topic:0748 ! Protein sites and features
is_obsolete: true !{since=1.0}
consider: EDAM_topic:0601 ! Protein modifications
consider: EDAM_topic:0748 ! Protein sites and features

[Term]
id: EDAM_topic:0753
name: Metabolic pathways
namespace: topic
subset: topics
def: "Topic concerning metabolic pathways." [http://edamontology.org]
is_a: EDAM_topic:0602 ! Pathways, networks and models
is_a: EDAM_topic:3172 ! Metabolomics


[Term]
id: EDAM_topic:0754
name: Signaling pathways
namespace: topic
subset: topics
def: "Topic concerning signaling pathways." [http://edamontology.org]
is_a: EDAM_topic:0602 ! Pathways, networks and models

[Term]
id: EDAM_topic:3044 {since=beta13}
name: Protein interaction networks
namespace: topic
subset: topics
def: "Topic concerning protein-protein interaction networks." [http://edamontology.org]
is_a: EDAM_topic:0602 ! Pathways, networks and models
is_a: EDAM_topic:0147 ! Protein-protein interactions

[Term]
id: EDAM_topic:0771
name: Biological models
namespace: topic
subset: topics
! alt_id: EDAM_topic:2267
! alt_id: EDAM_topic:2268
def: "Topic concerning mathematical or other models of biological processes." [http://edamontology.org]
comment: This includes databases of models and methods to construct or analyse a model.
xref: BioCatalogue:Model Creation
is_a: EDAM_topic:0602 ! Pathways, networks and models


[Term]
id: EDAM_topic:2846
name: Gene regulatory networks
namespace: topic
subset: topics
def: "Topic concerning gene regulatory networks." [http://edamontology.org]
is_a: EDAM_topic:0602 ! Pathways, networks and models
is_a: EDAM_topic:0204 ! Gene regulation


[Term]
id: EDAM_topic:0767
name: Protein and peptide identification
namespace: topic
subset: topics
! alt_id: EDAM_topic:0603
def: "Topic concerning protein and peptide identification including proteomics experiments such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays." [http://edamontology.org]
comment: This includes the results of any methods that separate, characterize and identify expressed proteins.
synonym: "Peptide identification and proteolysis" EXACT [http://edamontology.org]
synonym: "Proteomics data" EXACT [http://edamontology.org]
synonym: "Proteomics data resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:0121 ! Proteomics
is_a: EDAM_topic:0639 ! Protein sequence analysis
is_a: EDAM_topic:2225 ! Protein databases


[Term]
id: EDAM_topic:0141
name: Protein cleavage sites and proteolysis
namespace: topic
subset: topics
def: "Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence." [http://edamontology.org]
is_a: EDAM_topic:0639 ! Protein sequence analysis




[Term]
id: EDAM_topic:0769
name: Workflows
namespace: topic
subset: topics
def: "Topic concerning biological or biomedical analytical workflows or pipelines." [http://edamontology.org]
! is_a: EDAM_topic:0091 ! Data handling
is_obsolete: true !{since=1.0}
! consider: EDAM_topic:0003 ! Topic


[Term]
id: EDAM_topic:0220
name: Data processing and validation
namespace: topic
subset: topics
! alt_id: EDAM_topic:2286
! alt_id: EDAM_topic:2270
! alt_id: EDAM_topic:2834
def: "Topic concerning basic manipulations of files or reports of generic biological data." [http://edamontology.org]
comment: This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.
synonym: "Report handling" EXACT [http://edamontology.org]
synonym: "File handling" EXACT [http://edamontology.org]
synonym: "Data file handling" EXACT [http://edamontology.org]
synonym: "Report processing" EXACT [http://edamontology.org]
is_a: EDAM_topic:0091 ! Data handling

[Term]
id: EDAM_topic:0770
name: Data types and objects
namespace: topic
subset: topics
def: "Topic concerning structuring data into basic types and (computational) objects." [http://edamontology.org]
! is_a: EDAM_topic:0091 ! Data handling
is_obsolete: true !{since=1.0}
consider: EDAM_topic:0091 ! Data handling


[Term]
id: EDAM_topic:0632
name: Probes and primers
namespace: topic
subset: topics
! alt_id: EDAM_topic:0207
def: "Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR)." [http://edamontology.org]
is_a: EDAM_topic:0607 ! Laboratory resources
is_a: EDAM_topic:3041 ! Sequence databases


[Term]
id: EDAM_topic:3032 {since=beta13}
name: Primer or probe design
namespace: topic
subset: topics
def: "Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes." [http://edamontology.org]
is_a: EDAM_topic:0080 ! Sequence analysis



[Term]
id: EDAM_topic:0779
name: Mitochondrial genes and proteins
namespace: topic
subset: topics
def: "Topic concerning mitochondria, typically of mitochondrial genes and proteins." [http://edamontology.org]
synonym: "Mitochondria genes and proteins" EXACT [http://edamontology.org]
is_a: EDAM_topic:0616 ! Organelle genes and proteins


[Term]
id: EDAM_topic:2818
name: Eukaryotes
namespace: topic
subset: topics
! alt_id: EDAM_topic:0669
def: "Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
synonym: "Eukaryote" EXACT [http://edamontology.org]
is_a: EDAM_topic:0621 ! Genome, proteome and model organisms


[Term]
id: EDAM_topic:2821
name: Unicellular eukaryotes
namespace: topic
subset: topics
! alt_id: EDAM_topic:0675
def: "Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
synonym: "Unicellular eukaryote" EXACT [http://edamontology.org]
is_a: EDAM_topic:2818 ! Eukaryotes



[Term]
id: EDAM_topic:2819
name: Invertebrates
namespace: topic
subset: topics
! alt_id: EDAM_topic:0678
def: "Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
is_a: EDAM_topic:2818 ! Eukaryotes

[Term]
id: EDAM_topic:2820
name: Vertebrates
namespace: topic
subset: topics
! alt_id: EDAM_topic:0679
def: "Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
synonym: "Vertebrate" EXACT [http://edamontology.org]
is_a: EDAM_topic:2818 ! Eukaryotes

[Term]
id: EDAM_topic:2815
name: Humans
namespace: topic
subset: topics
! alt_id: EDAM_topic:0692
! alt_id: EDAM_topic:0687
def: "Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general." [http://edamontology.org]
comment: The resource may be specific to a human, a group of humans or all humans.
synonym: "Human" EXACT [http://edamontology.org]
is_a: EDAM_topic:3048 ! Mammals


[Term]
id: EDAM_topic:0780
name: Plants
namespace: topic
subset: topics
! alt_id: EDAM_topic:0677
! alt_id: EDAM_topic:0785
! alt_id: EDAM_topic:0784
! alt_id: EDAM_topic:0214
def: "Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a plant, a group of plants or all plants.
synonym: "Plant" EXACT [http://edamontology.org]
is_a: EDAM_topic:2818 ! Eukaryotes


[Term]
id: EDAM_topic:0781
name: Viruses
namespace: topic
subset: topics
! alt_id: EDAM_topic:0790
! alt_id: EDAM_topic:0671
! alt_id: EDAM_topic:0791
def: "Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a virus, a group of viruses or all viruses.
synonym: "Virus" EXACT [http://edamontology.org]
is_a: EDAM_topic:0621 ! Genome, proteome and model organisms


[Term]
id: EDAM_topic:0782
name: Fungi
namespace: topic
subset: topics
! alt_id: EDAM_topic:0792
! alt_id: EDAM_topic:0793
! alt_id: EDAM_topic:0676
def: "Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a fungus, a group of fungi or all fungi.
synonym: "Fungal" EXACT [http://edamontology.org]
is_a: EDAM_topic:2818 ! Eukaryotes


[Term]
id: EDAM_topic:0783
name: Pathogens
namespace: topic
subset: topics
def: "Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a pathogen, a group of pathogens or all pathogens.
synonym: "Pathogen" EXACT [http://edamontology.org]
is_a: EDAM_topic:0621 ! Genome, proteome and model organisms


[Term]
id: EDAM_topic:1811
name: Prokaryotes and archae
namespace: topic
subset: topics
! alt_id: EDAM_topic:0691
! alt_id: EDAM_topic:0670
! alt_id: EDAM_topic:0212
def: "Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation." [http://edamontology.org]
comment: The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
synonym: "Prokaryote and archae" EXACT [http://edamontology.org]
is_a: EDAM_topic:0621 ! Genome, proteome and model organisms

[Term]
id: EDAM_topic:0786
name: Arabidopsis
namespace: topic
subset: topics
def: "Topic concerning Arabidopsis-specific data." [http://edamontology.org]
is_a: EDAM_topic:0780 ! Plants

[Term]
id: EDAM_topic:0787
name: Rice
namespace: topic
subset: topics
def: "Topic concerning rice-specific data." [http://edamontology.org]
is_a: EDAM_topic:0780 ! Plants


[Term]
id: EDAM_topic:2817
name: Yeast
namespace: topic
subset: topics
! alt_id: EDAM_topic:0682
! alt_id: EDAM_topic:0216
def: "Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation." [http://edamontology.org]
is_a: EDAM_topic:0782 ! Fungi


[Term]
id: EDAM_topic:0796
name: Genetic mapping and linkage
namespace: topic
subset: topics
! alt_id: EDAM_topic:0103
def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [http://edamontology.org]
synonym: "Genetic linkage" EXACT [http://edamontology.org]
synonym: "Linkage mapping" EXACT [http://edamontology.org]
is_a: EDAM_topic:0102 ! Mapping
relationship: has_topic EDAM_topic:3053 ! Genetics


[Term]
id: EDAM_topic:0797
name: Comparative genomics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0101
def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org]
xref: BioCatalogue:Comparative Genomics
is_a: EDAM_topic:0622 ! Genomics


[Term]
id: EDAM_topic:0798
name: Mobile genetic elements
namespace: topic
subset: topics
def: "Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns." [http://edamontology.org]
is_a: EDAM_topic:3062 ! Genetic organisation


! [Term]
! id: EDAM_topic:0801
! name: Human genes
! namespace: resources
! def: "Topic concerning human genes." [http://edamontology.org]
! is_obsolete: true !{since=beta12orEarlier}
! consider: EDAM_topic:0623 ! Genes, gene family or system


[Term]
id: EDAM_topic:0803
name: Human disease
namespace: topic
subset: topics
def: "Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_topic:0634 ! Disease resources

[Term]
id: EDAM_topic:0804
name: Immunoinformatics
namespace: topic
subset: topics
! alt_id: EDAM_topic:0201
! alt_id: EDAM_topic:0633
def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org]
synonym: "Computational immunology" EXACT [http://edamontology.org]
is_a: EDAM_topic:0003 ! Topic

[Term]
id: EDAM_topic:2830
name: Immunity genes, immunoproteins and antigens
namespace: topic
subset: topics
def: "Topic concerning immunity-related genes, proteins and their ligands." [http://edamontology.org]
comment: This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
synonym: "Immunoproteins and immunopeptides" EXACT [http://edamontology.org]
is_a: EDAM_topic:0804 ! Immunoinformatics
is_a: EDAM_topic:3078 ! Gene and protein resources


[Term]
id: EDAM_topic:2847
name: Disease (specific)
namespace: topic
subset: topics
def: "Informatics resources dedicated to one or more specific diseases (not diseases in general)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_topic:0634 ! Disease resources

[Term]
id: EDAM_topic:2640
name: Cancer
namespace: topic
subset: topics
! alt_id: EDAM_topic:0805
def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org]
synonym: "Cancer resources" EXACT [http://edamontology.org]
is_a: EDAM_topic:0634 ! Disease resources



[Term]
id: EDAM_topic:0820
name: Membrane proteins
namespace: topic
subset: topics
! alt_id: EDAM_topic:0131
def: "Topic concerning a protein or region of a protein that spans a membrane." [http://edamontology.org]
synonym: "Transmembrane proteins" EXACT [http://edamontology.org]
is_a: EDAM_topic:0635 ! Specific protein resources

[Term]
id: EDAM_topic:0821
name: Enzymes and reactions
namespace: topic
subset: topics
! alt_id: EDAM_topic:0132
def: "Topic concerning proteins that catalyze chemical reaction and the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc." [http://edamontology.org]
is_a: EDAM_topic:0635 ! Specific protein resources








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!
! Operation
!


[Term]
id: EDAM_operation:2945
name: Analysis
namespace: operation
subset: operations
def: "Apply analytical methods to existing data of a specific type." [http://edamontology.org]
comment: For non-analytical operations, see the 'Processing' branch.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2420 ! Analysis and processing

[Term]
id: EDAM_operation:2420
name: Analysis and processing
namespace: operation
subset: operations
def: "Process (read and / or write) data of a specific type, for example applying analytical methods." [http://edamontology.org]
synonym: "Calculation" EXACT [http://edamontology.org]
synonym: "Computation" EXACT [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation
relationship: has_input EDAM_data:0006 {min_cardinality=0} ! Data
relationship: has_output EDAM_data:0006 {min_cardinality=0} ! Data

[Term]
id: EDAM_operation:2423
name: Prediction, detection and recognition
namespace: operation
subset: operations
def: "Predict, recognise, detect or identify some properties of a biomolecule." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation

[Term]
id: EDAM_operation:3023
name: Prediction, detection and recognition (protein)
namespace: operation
subset: operations
def: "Predict, recognise, detect or identify some properties of proteins." [http://edamontology.org]
is_a: EDAM_operation:2423 ! Prediction, detection and recognition

[Term]
id: EDAM_operation:3024
name: Prediction, detection and recognition (nucleic acid)
namespace: operation
subset: operations
def: "Predict, recognise, detect or identify some properties of nucleic acids." [http://edamontology.org]
is_a: EDAM_operation:2423 ! Prediction, detection and recognition


[Term]
id: EDAM_operation:2946
name: Alignment analysis
namespace: operation
subset: operations
def: "Analyse an existing alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org]
is_a: EDAM_operation:2951 ! Alignment processing
relationship: has_input EDAM_data:1916 {min_cardinality=1} ! Alignment  ! Extends cardinality constraint on parent.
relationship: has_output EDAM_data:2083 {min_cardinality=1} ! Alignment report

[Term]
id: EDAM_operation:2947
name: Article analysis
namespace: operation
subset: operations
def: "Analyse a body of scientific text (typically a full text article from a scientific journal.)" [http://edamontology.org]
is_a: EDAM_operation:2505 ! Text processing
relationship: has_input EDAM_data:0971 {min_cardinality=1} ! Article
relationship: has_output EDAM_data:2954 ! Article report
relationship: has_topic EDAM_topic:0217 ! Literature analysis

[Term]
id: EDAM_operation:2993
name: Molecular interaction data processing
namespace: operation
subset: operations
def: "Process (read and / or write) molecular interaction data." [http://edamontology.org]
is_obsolete: true !{since=beta13}


[Term]
id: EDAM_operation:2948
name: Molecular interaction analysis
namespace: operation
subset: operations
def: "Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact." [http://edamontology.org]
is_obsolete: true !{since=beta13}

[Term]
id: EDAM_operation:2949
name: Protein interaction analysis
namespace: operation
subset: operations
def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org]
is_a: EDAM_operation:2405 ! Protein interaction data processing
relationship: has_output EDAM_data:0906 {min_cardinality=1} ! Protein interaction
relationship: has_topic EDAM_topic:0128 ! Protein interactions


[Term]
id: EDAM_operation:3096 {since=beta13}
name: Editing
namespace: operation
subset: operations
def: "Edit, convert or otherwise change a data entity, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation



[Term]
id: EDAM_operation:2928
name: Alignment construction
namespace: operation
subset: operations
def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org]
synonym: "Alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2951 ! Alignment processing
relationship: has_output EDAM_data:1916 {min_cardinality=1} ! Alignment

[Term]
id: EDAM_operation:2424
name: Comparison
namespace: operation
subset: operations
def: "Compare two or more things to identify similarities." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation

[Term]
id: EDAM_operation:2997
name: Protein comparison
namespace: operation
subset: operations
def: "Compare two or more proteins (or some aspect) to identify similarities." [http://edamontology.org]
is_a: EDAM_operation:2424 ! Comparison

[Term]
id: EDAM_operation:2998
name: Nucleic acid comparison
namespace: operation
subset: operations
def: "Compare two or more nucleic acids to identify similarities." [http://edamontology.org]
is_a: EDAM_operation:2424 ! Comparison

[Term]
id: EDAM_operation:2990
name: Classification
namespace: operation
subset: operations
def: "Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation
relationship: has_output EDAM_data:2987 {min_cardinality=1} ! Classification

[Term]
id: EDAM_operation:2995
name: Sequence classification
namespace: operation
subset: operations
def: "Assign molecular sequence(s) to a group or category." [http://edamontology.org]
is_a: EDAM_operation:2990 ! Classification
is_a: EDAM_operation:2403 ! Sequence analysis


[Term]
id: EDAM_operation:3093 {since=beta13}
name: Sequence screening
namespace: operation
subset: operations
def: "Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries." [http://edamontology.org]
is_a: EDAM_operation:2995 ! Sequence classification





[Term]
id: EDAM_operation:2996
name: Structure classification
namespace: operation
subset: operations
def: "Assign molecular structure(s) to a group or category." [http://edamontology.org]
is_a: EDAM_operation:2990 ! Classification
is_a: EDAM_operation:2480 ! Structure analysis


[Term]
id: EDAM_operation:2425
name: Optimisation and refinement
namespace: operation
subset: operations
def: "Refine or optimise some data model." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation

[Term]
id: EDAM_operation:2426
name: Modelling and simulation
namespace: operation
subset: operations
def: "Model or simulate some biological entity or system." [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation
relationship: has_topic EDAM_topic:2275 ! Molecular modelling


[Term]
id: EDAM_operation:2427
name: Data handling
namespace: operation
subset: operations
def: "Perform basic operations on some data or a database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2420 ! Analysis and processing


[Term]
id: EDAM_operation:2428
name: Evaluation and validation
namespace: operation
subset: operations
def: "Validate or standardise some data." [http://edamontology.org]
synonym: "Validation and standardisation" EXACT [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation


[Term]
id: EDAM_operation:2429
name: Mapping and assembly
namespace: operation
subset: operations
def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org]
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
is_a: EDAM_operation:0004 ! Operation
relationship: has_topic EDAM_topic:0102 ! Mapping
relationship: has_topic EDAM_topic:0196 ! Sequence assembly

[Term]
id: EDAM_operation:2430
name: Design
namespace: operation
subset: operations
def: "Design a biological entity (typically a molecular sequence or structure) with specific properties." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)


[Term]
id: EDAM_operation:2238
name: Statistical calculation
namespace: operation
subset: operations
def: "Perform a statistical data operation of some type, e.g. calibration or validation." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0004 ! Operation

[Term]
id: EDAM_operation:0224
name: Search and retrieval
namespace: operation
subset: operations
def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org]
synonym: "Database retrieval" EXACT [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation
relationship: has_output EDAM_data:0006 {min_cardinality=0} ! Data
relationship: has_topic EDAM_topic:0090 ! Data search and retrieval

[Term]
id: EDAM_operation:2501
name: Nucleic acid data processing
namespace: operation
subset: operations
def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2084 {min_cardinality=0} ! Nucleic acid report
relationship: has_output EDAM_data:2084 {min_cardinality=0} ! Nucleic acid report
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis


[Term]
id: EDAM_operation:2502
name: Protein data processing
namespace: operation
subset: operations
def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:0896 {min_cardinality=0} ! Protein report
relationship: has_output EDAM_data:0896 {min_cardinality=0} ! Protein report
relationship: has_topic EDAM_topic:0078 ! Protein analysis


[Term]
id: EDAM_operation:2407
name: Annotation processing
namespace: operation
subset: operations
def: "Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:2951
name: Alignment processing
namespace: operation
subset: operations
def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1916 {min_cardinality=0} ! Alignment
relationship: has_output EDAM_data:1916 {min_cardinality=0} ! Alignment



[Term]
id: EDAM_operation:2412
name: Data index processing
namespace: operation
subset: operations
def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org]
synonym: "Database index processing" EXACT [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing
relationship: has_input EDAM_data:0955 {min_cardinality=0} ! Data index
relationship: has_output EDAM_data:0955 {min_cardinality=0} ! Data index
relationship: has_topic EDAM_topic:0220 ! Data processing and validation

[Term]
id: EDAM_operation:2504
name: Structural data processing
namespace: operation
subset: operations
def: "Process (read and / or write) molecular structural data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2465 ! Structure processing


[Term]
id: EDAM_operation:2403
name: Sequence analysis
namespace: operation
subset: operations
! alt_id: EDAM_operation:2477
def: "Analyse one or more known molecular sequences." [http://edamontology.org]
synonym: "Sequence analysis (general)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
relationship: has_output EDAM_data:2955 {min_cardinality=1} ! Sequence report
relationship: has_topic EDAM_topic:0080 ! Sequence analysis

[Term]
id: EDAM_operation:2408
name: Sequence feature analysis
namespace: operation
subset: operations
def: "Analyse features in molecular sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0253 ! Feature prediction


[Term]
id: EDAM_operation:2404
name: Sequence motif processing
namespace: operation
subset: operations
def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_output EDAM_data:1353 {min_cardinality=0} ! Sequence motif
relationship: has_topic EDAM_topic:0158 ! Sequence motifs


[Term]
id: EDAM_operation:2417
name: Physicochemical property data processing
namespace: operation
subset: operations
def: "Process (read and / or write) data on the physicochemical property of a molecule." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2420 ! Analysis and processing


[Term]
id: EDAM_operation:2414
name: Protein function analysis
namespace: operation
subset: operations
def: "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report." [http://edamontology.org]
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_output EDAM_data:0896 ! Protein report

[Term]
id: EDAM_operation:0258
name: Sequence alignment analysis
namespace: operation
subset: operations
def: "Analyse a molecular sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:2463 ! Sequence alignment processing
is_a: EDAM_operation:2946 ! Alignment analysis
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment ! Extends cardinality constraint on parent.
relationship: has_output EDAM_data:0867 {min_cardinality=1} ! Sequence alignment report
relationship: has_topic EDAM_topic:0182 ! Sequence alignment


[Term]
id: EDAM_operation:2506
name: Sequence alignment analysis (protein)
namespace: operation
subset: operations
def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org]
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2502 ! Protein data processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_input EDAM_data:1384 {min_cardinality=1} ! Sequence alignment (protein)
relationship: has_topic EDAM_topic:0741 ! Protein sequence alignment

[Term]
id: EDAM_operation:2507
name: Sequence alignment analysis (nucleic acid)
namespace: operation
subset: operations
def: "Analyse a protein sequence alignment, typically to detect features or make predictions." [http://edamontology.org]
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2501 ! Nucleic acid data processing
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_input EDAM_data:1383 {min_cardinality=1} ! Sequence alignment (nucleic acid)
relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment

[Term]
id: EDAM_operation:2416
name: Protein secondary structure analysis
namespace: operation
subset: operations
def: "Analyse known protein secondary structure data." [http://edamontology.org]
is_a: EDAM_operation:2444 ! Protein secondary structure processing
synonym: "Secondary structure analysis (protein)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:0876 {min_cardinality=1} ! Protein features (secondary structure)
relationship: has_output EDAM_data:2956 ! Protein secondary structure report
relationship: has_topic EDAM_topic:0694 ! Protein secondary structure


[Term]
id: EDAM_operation:0270
name: Transmembrane protein analysis
namespace: operation
subset: operations
def: "Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions." [http://edamontology.org]
comment: Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_output EDAM_data:1456 ! Protein features (membrane regions)
relationship: has_topic EDAM_topic:0820 ! Membrane proteins


[Term]
id: EDAM_operation:2476
name: Molecular dynamics simulation
namespace: operation
subset: operations
def: "Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation." [http://edamontology.org]
is_a: EDAM_operation:2423 ! Prediction, detection and recognition
is_a: EDAM_operation:2480 ! Structure analysis
is_a: EDAM_operation:2426 ! Modelling and simulation
relationship: has_output EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0082 ! Structure prediction
relationship: has_topic EDAM_topic:0176 ! Molecular dynamics


[Term]
id: EDAM_operation:0271
name: Structure prediction
namespace: operation
subset: operations
def: "Predict tertiary structure of a molecular (biopolymer) sequence." [http://edamontology.org]
is_a: EDAM_operation:2423 ! Prediction, detection and recognition
is_a: EDAM_operation:2465 ! Structure processing
relationship: has_output EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0082 ! Structure prediction


[Term]
id: EDAM_operation:2405
name: Protein interaction data processing
namespace: operation
subset: operations
def: "Process (read and / or write) protein interaction data." [http://edamontology.org]
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_input EDAM_data:0906 {min_cardinality=0} ! Protein interaction
relationship: has_output EDAM_data:0906 {min_cardinality=0} ! Protein interaction
relationship: has_topic EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_operation:2521
name: Map data processing
namespace: operation
subset: operations
def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org]
synonym: "DNA map data processing" EXACT [http://edamontology.org]
is_a: EDAM_operation:2501 ! Nucleic acid data processing
relationship: has_input EDAM_data:1274 {min_cardinality=0} ! Map
relationship: has_output EDAM_data:1274 {min_cardinality=0} ! Map
relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage



[Term]
id: EDAM_operation:3229 {since=1.1}
name: Exome analysis
namespace: operation
subset: operations
def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org]
comment: Exome sequencing is considered a cheap alternative to whole genome sequencing.
synonym: "Exome sequence analysis" EXACT [http://edamontology.org]
synonym: "Targeted exome capture" EXACT [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:3230 {since=1.1}
name: Read depth analysis
namespace: operation
subset: operations
def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:3225 {since=1.1}
name: Variant classification
namespace: operation
subset: operations
def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org]
comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:2995 ! Sequence classification

[Term]
id: EDAM_operation:3226 {since=1.1}
name: Variant prioritization
namespace: operation
subset: operations
def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org]
comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis

[Term]
id: EDAM_operation:3221 {since=1.1}
name: Species frequency estimation
namespace: operation
subset: operations
def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_topic EDAM_topic:3174 ! Metagenomics



[Term]
id: EDAM_operation:3216 {since=1.1}
name: Scaffolding
namespace: operation
subset: operations
def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length.  The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org]
comment: Scaffold may be positioned along a chromosome physical map to create a "golden path".
synonym: "Scaffold construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2429 ! Mapping and assembly
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis

[Term]
id: EDAM_operation:3217 {since=1.1}
name: Scaffold gap completion
namespace: operation
subset: operations
def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org]
comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used.  For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. 
is_a: EDAM_operation:2429 ! Mapping and assembly
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis



[Term]
id: EDAM_operation:3218 {since=1.1}
name: Sequencing quality control
namespace: operation
subset: operations
def: "Raw sequence data quality control." [http://edamontology.org]
synonym: "Sequencing QC" EXACT [http://edamontology.org]
synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:2428 ! Evaluation and validation


[Term]
id: EDAM_operation:2520
name: DNA mapping
namespace: operation
subset: operations
def: "Generate a map of a DNA sequence annotated with positional or non-positional features of some type." [http://edamontology.org]
is_a: EDAM_operation:2521 ! Map data processing
is_a: EDAM_operation:2429 ! Mapping and assembly
relationship: has_output EDAM_data:1274 {min_cardinality=1} ! Map
relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage

[Term]
id: EDAM_operation:0282
name: Genetic mapping
namespace: operation
subset: operations
def: "Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances." [http://edamontology.org]
comment: Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.
synonym: "Genetic map generation" EXACT [http://edamontology.org]
synonym: "Linkage mapping" EXACT [http://edamontology.org]
is_a: EDAM_operation:2520 ! DNA mapping
relationship: has_output EDAM_data:1278 {min_cardinality=1} ! Genetic map
relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage


[Term]
id: EDAM_operation:2944
name: Physical mapping
namespace: operation
subset: operations
def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [http://edamontology.org]
is_a: EDAM_operation:2520 ! DNA mapping
relationship: has_output EDAM_data:1280 {min_cardinality=1} ! Physical map
relationship: has_topic EDAM_topic:0102 ! Mapping


[Term]
id: EDAM_operation:2871
name: Sequence tagged site (STS) mapping
namespace: operation
subset: operations
def: "Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS)." [http://edamontology.org]
comment: An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
synonym: "Sequence mapping" EXACT [http://edamontology.org]
is_a: EDAM_operation:2944 ! Physical mapping
relationship: has_output EDAM_data:1279 {min_cardinality=1} ! Sequence map



[Term]
id: EDAM_operation:3233 {since=1.1}
name: Copy number estimation
namespace: operation
subset: operations
def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org]
comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).
synonym: "Transcript copy number estimation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis

[Term]
id: EDAM_operation:3219 {since=1.1}
name: Read pre-processing
namespace: operation
subset: operations
def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org]
comment: This is a broad concept and is used a placeholder for other, more specific concepts.  For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
synonym: "Sequence read pre-processing" EXACT [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:0283
name: Linkage analysis
namespace: operation
subset: operations
def: "Analyse genetic linkage." [http://edamontology.org]
comment: For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_output EDAM_data:0927 ! Gene annotation (linkage)
relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage

[Term]
id: EDAM_operation:2493
name: Codon usage data processing
namespace: operation
subset: operations
def: "Process (read and / or write) codon usage data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0286 ! Codon usage analysis



[Term]
id: EDAM_operation:2503
name: Sequence data processing
namespace: operation
subset: operations
def: "Process (read and / or write) molecular sequence data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2446 ! Sequence processing


[Term]
id: EDAM_operation:2463
name: Sequence alignment processing
namespace: operation
subset: operations
def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:2951 ! Alignment processing
relationship: has_input EDAM_data:0863 {min_cardinality=0} ! Sequence alignment
relationship: has_output EDAM_data:0863 {min_cardinality=0} ! Sequence alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_operation:2952
name: Structure alignment processing
namespace: operation
subset: operations
def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org]
is_a: EDAM_operation:2951 ! Alignment processing
relationship: has_input EDAM_data:0886 {min_cardinality=0} ! Structure alignment
relationship: has_output EDAM_data:0886 {min_cardinality=0} ! Structure alignment
relationship: has_topic EDAM_topic:0183 ! Structure alignment


[Term]
id: EDAM_operation:0292
name: Sequence alignment construction
namespace: operation
subset: operations
def: "Align (identify equivalent sites within) molecular sequences." [http://edamontology.org]
synonym: "Sequence alignment" EXACT [http://edamontology.org]
synonym: "Sequence alignment computation" EXACT [http://edamontology.org]
synonym: "Sequence alignment generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2463 ! Sequence alignment processing !(?)
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:2044 {minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence
relationship: has_output EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_operation:0293
name: Hybrid sequence alignment construction
namespace: operation
subset: operations
def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org]
synonym: "Hybrid sequence alignment" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0292 ! Sequence alignment construction

[Term]
id: EDAM_operation:0294
name: Structure-based sequence alignment construction
namespace: operation
subset: operations
def: "Align molecular sequences using sequence and structural information." [http://edamontology.org]
synonym: "Structure-based sequence alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0292 ! Sequence alignment construction
relationship: has_topic EDAM_topic:0182 ! Sequence alignment



[Term]
id: EDAM_operation:2480
name: Structure analysis
namespace: operation
subset: operations
! alt_id: EDAM_operation:2431
def: "Analyse known molecular tertiary structures." [http://edamontology.org]
is_a: EDAM_operation:2465 ! Structure processing
relationship: has_input EDAM_data:0883 {min_cardinality=1} ! Structure
relationship: has_output EDAM_data:2085 {min_cardinality=1} ! Structure report
relationship: has_topic EDAM_topic:0081 ! Structure analysis

[Term]
id: EDAM_operation:2931
name: Secondary structure comparison
namespace: operation
subset: operations
def: "Compare two or more molecular secondary structures." [http://edamontology.org]
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:2081 {min_cardinality=2} ! Secondary structure
relationship: has_output EDAM_data:2881 {min_cardinality=1} ! Secondary structure report
relationship: has_topic EDAM_topic:1770 ! Structure comparison

[Term]
id: EDAM_operation:2483
name: Structure comparison
namespace: operation
subset: operations
def: "Compare two or more molecular tertiary structures." [http://edamontology.org]
is_a: EDAM_operation:2424 ! Comparison
is_a: EDAM_operation:2480 ! Structure analysis
relationship: has_topic EDAM_topic:1770 ! Structure comparison


[Term]
id: EDAM_operation:0295
name: Structure alignment construction
namespace: operation
subset: operations
def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org]
synonym: "Structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2928 ! Alignment construction
is_a: EDAM_operation:2483 ! Structure comparison
is_a: EDAM_operation:2952 ! Structure alignment processing
relationship: has_output EDAM_data:0886 {min_cardinality=1} ! Structure alignment
relationship: has_topic EDAM_topic:0183 ! Structure alignment

[Term]
id: EDAM_operation:2413
name: Sequence profile processing
namespace: operation
subset: operations
def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1354 {min_cardinality=0} ! Sequence profile
relationship: has_output EDAM_data:1354 {min_cardinality=0} ! Sequence profile
relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs

[Term]
id: EDAM_operation:2411
name: Structural (3D) profile processing
namespace: operation
subset: operations
def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:0889 {min_cardinality=0} ! Structural (3D) profile
relationship: has_output EDAM_data:0889 {min_cardinality=0} ! Structural (3D) profile
relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles


[Term]
id: EDAM_operation:0303
name: Protein fold recognition
namespace: operation
subset: operations
def: "Recognize (predict and identify) known protein structural domains or folds in protein sequence(s)." [http://edamontology.org]
comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
synonym: "Protein domain prediction" EXACT [http://edamontology.org]
synonym: "Protein fold prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence)
is_a: EDAM_operation:0474 ! Protein structure prediction
is_a: EDAM_operation:2997 ! Protein comparison
relationship: has_output EDAM_data:0901 {min_cardinality=1} ! Protein features (domains)
relationship: has_topic EDAM_topic:0184 ! Threading

[Term]
id: EDAM_operation:2246
name: Demonstration
namespace: operation
subset: operations
def: "An operation performing purely illustrative (pedagogical) purposes." [http://edamontology.org]
is_obsolete: true !{since=beta13}

[Term]
id: EDAM_operation:2505
name: Text processing
namespace: operation
subset: operations
def: "Process (read and / or write) text." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2048 {min_cardinality=0} ! Report
relationship: has_output EDAM_data:2048 {min_cardinality=0} ! Report

[Term]
id: EDAM_operation:0306
name: Text mining
namespace: operation
subset: operations
def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org]
synonym: "Text data mining" EXACT [http://edamontology.org]
is_a: EDAM_operation:2947 ! Article analysis
relationship: has_input EDAM_data:2048 {min_cardinality=0} ! Report
relationship: has_output EDAM_data:0972 ! Text mining report
relationship: has_topic EDAM_topic:0218 ! Text mining

[Term]
id: EDAM_operation:2419
name: Primer and probe design
namespace: operation
subset: operations
def: "Predict oligonucleotide primers or probes." [http://edamontology.org]
is_a: EDAM_operation:3095 ! Nucleic acid design
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
synonym: "Primer and probe prediction" EXACT [http://edamontology.org]
relationship: has_topic EDAM_topic:3032 ! Primer or probe design

[Term]
id: EDAM_operation:0310
name: Sequence assembly
namespace: operation
subset: operations
def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org]
comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
is_a: EDAM_operation:2429 ! Mapping and assembly
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_output EDAM_data:0925 ! Sequence assembly
relationship: has_topic EDAM_topic:0196 ! Sequence assembly

[Term]
id: EDAM_operation:3180 {since=1.1}
name: Sequence assembly evaluation
namespace: operation
subset: operations
def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org]
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_input EDAM_data:0925 ! Sequence assembly
relationship: has_output EDAM_data:3181 ! Sequence assembly report
relationship: has_topic EDAM_topic:0196 ! Sequence assembly


[Term]
id: EDAM_operation:2432
name: Microarray data processing
namespace: operation
subset: operations
def: "Process (read and / or write) microarray data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing

[Term]
id: EDAM_operation:2495
name: Gene expression data processing
namespace: operation
subset: operations
def: "Process (read and / or write) gene expression (typically microarray) data." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
synonym: "Gene expression (microarray) data processing" EXACT [http://edamontology.org]
synonym: "Microarray data processing" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:3117 {min_cardinality=0} ! Microarray hybridisation data
relationship: has_output EDAM_data:3117 {min_cardinality=0} ! Microarray hybridisation data
relationship: has_topic EDAM_topic:0203 ! Transcriptomics
relationship: has_topic EDAM_topic:0200 ! Microarrays


[Term]
id: EDAM_operation:2500
name: Microarray raw data analysis
namespace: operation
subset: operations
def: "Analyse raw microarray data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing

[Term]
id: EDAM_operation:0311
name: Microarray data standardization and normalization
namespace: operation
subset: operations
def: "Standardize or normalize microarray data." [http://edamontology.org]
comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.
is_a: EDAM_operation:2495 ! Gene expression data processing
is_a: EDAM_operation:2428 ! Evaluation and validation
relationship: has_input EDAM_data:3117 {min_cardinality=1} ! Microarray hybridisation data
relationship: has_output EDAM_data:3117 {min_cardinality=1} ! Microarray hybridisation data

[Term]
id: EDAM_operation:0318
name: Structural genomics target selection
namespace: operation
subset: operations
def: "Identify and select targets for protein structural determination." [http://edamontology.org]
comment: Methods will typically navigate a graph of protein families of known structure.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2406 ! Protein structure analysis

[Term]
id: EDAM_operation:2406
name: Protein structure analysis
namespace: operation
subset: operations
! alt_id: EDAM_operation:2458
def: "Analyse protein tertiary structural data." [http://edamontology.org]
is_a: EDAM_operation:2480 ! Structure analysis
is_a: EDAM_operation:2459 ! Structure processing (protein)
synonym: "Structure analysis (protein)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:1460 {min_cardinality=1} ! Protein structure
relationship: has_output EDAM_data:0897 ! Protein property


[Term]
id: EDAM_operation:2481
name: Nucleic acid structure analysis
namespace: operation
subset: operations
! alt_id: EDAM_operation:2418
def: "Analyse nucleic acid tertiary structural data." [http://edamontology.org]
is_a: EDAM_operation:2480 ! Structure analysis
is_a: EDAM_operation:2519 ! Structure processing (nucleic acid)
relationship: has_input EDAM_data:1459 {min_cardinality=1} ! Nucleic acid structure
relationship: has_output EDAM_data:0912 {min_cardinality=1} ! Nucleic acid property

[Term]
id: EDAM_operation:0324
name: Phylogenetic tree analysis
namespace: operation
subset: operations
def: "Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions." [http://edamontology.org]
is_a: EDAM_operation:2443 ! Phylogenetic tree processing
relationship: has_input EDAM_data:0872 {min_cardinality=1} ! Phylogenetic tree
relationship: has_output EDAM_data:1438 {min_cardinality=1} ! Phylogenetic tree report

[Term]
id: EDAM_operation:2438
name: Pathway or network processing
namespace: operation
subset: operations
def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2600 {min_cardinality=0} ! Pathway or network
relationship: has_output EDAM_data:2600 {min_cardinality=0} ! Pathway or network
relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models

[Term]
id: EDAM_operation:3083 {since=beta13}
name: Pathway or network rendering
namespace: operation
subset: operations
def: "Render (visualise) a biological pathway or network." [http://edamontology.org]
is_a: EDAM_operation:2438 ! Pathway or network processing
is_a: EDAM_operation:0337 ! Plotting and rendering
relationship: has_input EDAM_data:2600 {min_cardinality=1} ! Pathway or network
relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models


[Term]
id: EDAM_operation:3203 {since=1.1}
name: Chromatogram visualisation
namespace: operation
subset: operations
def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org]
synonym: "Chromatogram viewing" EXACT [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering




[Term]
id: EDAM_operation:2497
name: Pathway or network analysis
namespace: operation
subset: operations
def: "Analyse a known biological pathway or network." [http://edamontology.org]
synonym: "Network analysis" EXACT [http://edamontology.org]
synonym: "Pathway analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:2438 ! Pathway or network processing
relationship: has_input EDAM_data:2600 {min_cardinality=1} ! Pathway or network
relationship: has_output EDAM_data:2984 {min_cardinality=1} ! Pathway or network report

[Term]
id: EDAM_operation:2415
name: Protein folding analysis
namespace: operation
subset: operations
def: "Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report." [http://edamontology.org]
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
synonym: "Protein folding modelling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2502 ! Protein data processing
is_a: EDAM_operation:2426 ! Modelling and simulation
relationship: has_output EDAM_data:0903 {min_cardinality=1} ! Protein folding report
relationship: has_topic EDAM_topic:0130 ! Protein folding and stability


[Term]
id: EDAM_operation:0331
name: Protein modelling (mutation)
namespace: operation
subset: operations
def: "Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function." [http://edamontology.org]
comment: Methods might predict silent or pathological mutations.
is_a: EDAM_operation:0477 ! Protein modelling
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
synonym: "Protein mutation modelling" EXACT [http://edamontology.org]
relationship: has_topic EDAM_topic:0130 ! Protein folding and stability
relationship: has_topic EDAM_topic:0199 ! Genetic variation

[Term]
id: EDAM_operation:0332
name: Immunogen design
namespace: operation
subset: operations
def: "Design molecules that elicit an immune response (immunogens)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0559 ! Peptide immunogen prediction and optimisation


[Term]
id: EDAM_operation:2409
name: File processing
namespace: operation
subset: operations
def: "Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations." [http://edamontology.org]
synonym: "Report handling" EXACT [http://edamontology.org]
synonym: "File handling" EXACT [http://edamontology.org]
synonym: "Data file processing" EXACT [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:0006 {min_cardinality=0} ! Data
relationship: has_output EDAM_data:0006 {min_cardinality=0} ! Data
relationship: has_topic EDAM_topic:0220 ! Data processing and validation


[Term]
id: EDAM_operation:0337
name: Plotting and rendering
namespace: operation
subset: operations
def: "Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures." [http://edamontology.org]
synonym: "Visualisation" EXACT [http://edamontology.org]
is_a: EDAM_operation:0004 ! Operation
relationship: has_input EDAM_data:0006 {min_cardinality=1} ! Data
relationship: has_output EDAM_data:2968 {min_cardinality=0} ! Image
relationship: has_topic EDAM_topic:0092 ! Data visualisation


[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_operation:3081 {since=beta13}
name: Sequence alignment editing
namespace: operation
subset: operations
def: "Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:2122 ! Sequence alignment file processing
is_a: EDAM_operation:3096 ! Editing

[Term]
id: EDAM_operation:2122
name: Sequence alignment file processing
namespace: operation
subset: operations
def: "Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences." [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing
is_a: EDAM_operation:2463 ! Sequence alignment processing
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
relationship: has_output EDAM_data:0863 {min_cardinality=1} ! Sequence alignment





[Term]
id: EDAM_operation:3080 {since=beta13}
name: Structure editing
namespace: operation
subset: operations
def: "Edit, convert or otherwise change a  molecular tertiary structure, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:2234 ! Structure file processing
is_a: EDAM_operation:3096 ! Editing
relationship: has_input EDAM_data:0883 {min_cardinality=1} ! Structure

[Term]
id: EDAM_operation:2234
name: Structure file processing
namespace: operation
subset: operations
def: "Perform basic (non-analytical) operations on a file of molecular tertiary structural data." [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing
is_a: EDAM_operation:2465 ! Structure processing



[Term]
id: EDAM_operation:2120
name: Listfile processing
namespace: operation
subset: operations
def: "Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses)." [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing
relationship: has_input EDAM_data:1111 ! EMBOSS listfile
relationship: has_output EDAM_data:1111 ! EMBOSS listfile


[Term]
id: EDAM_operation:1812
name: Data loading
namespace: operation
subset: operations
def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org]
synonym: "Database submission" EXACT [http://edamontology.org]
synonym: "Data submission" EXACT [http://edamontology.org]
xref: WHATIF:UploadPDB
is_a: EDAM_operation:2409 ! File processing
relationship: has_input EDAM_data:0842 {min_cardinality=1} ! Identifier

[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:0336
name: File validation
namespace: operation
subset: operations
def: "Test and validate the format and content of a data file." [http://edamontology.org]
is_a: EDAM_operation:2409 ! File processing
is_a: EDAM_operation:2428 ! Evaluation and validation


[Term]
id: EDAM_operation:2421
name: Database search
namespace: operation
subset: operations
def: "Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query." [http://edamontology.org]
comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.
is_a: EDAM_operation:0224 ! Search and retrieval
is_a: EDAM_operation:2424 ! Comparison
relationship: has_output EDAM_data:2080 {min_cardinality=0} ! Database hits

[Term]
id: EDAM_operation:2422
name: Data retrieval
namespace: operation
subset: operations
def: "Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords." [http://edamontology.org]
synonym: "Information retrieval" BROAD [http://edamontology.org]
is_a: EDAM_operation:0224 ! Search and retrieval
relationship: has_input EDAM_data:0842 {min_cardinality=1} ! Identifier

[Term]
id: EDAM_operation:0343
name: Transmembrane protein database search
namespace: operation
subset: operations
def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2421 ! Database search

[Term]
id: EDAM_operation:0304
name: Data retrieval (metadata and documentation)
namespace: operation
subset: operations
def: "Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described." [http://edamontology.org]
comment: This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
synonym: "Data retrieval (documentation)" EXACT [http://edamontology.org]
synonym: "Data retrieval (metadata)" EXACT [http://edamontology.org]
relationship: has_output EDAM_data:2337 {min_cardinality=1} ! Metadata
is_a: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:0225
name: Data retrieval (database cross-reference)
namespace: operation
subset: operations
def: "Search database to retrieve all relevant references to a particular entity or entry." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:1813
name: Sequence retrieval
namespace: operation
subset: operations
def: "Query a sequence data resource (typically a database) and retrieve sequences and / or annotation." [http://edamontology.org]
comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence

[Term]
id: EDAM_operation:1814
name: Structure retrieval
namespace: operation
subset: operations
def: "Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation." [http://edamontology.org]
comment: This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
xref: WHATIF:DownloadPDB
xref: WHATIF:EchoPDB
is_a: EDAM_operation:2422 ! Data retrieval
is_a: EDAM_operation:2465 ! Structure processing
relationship: has_output EDAM_data:0883 {min_cardinality=0} ! Structure


[Term]
id: EDAM_operation:2237
name: Data retrieval (sequence profile)
namespace: operation
subset: operations
def: "Query a profile data resource and retrieve one or more profile(s) and / or associated annotation." [http://edamontology.org]
comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:2434
name: Data retrieval (codon usage table)
namespace: operation
subset: operations
def: "Retrieve a codon usage table and / or associated annotation." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2264
name: Data retrieval (pathway or network)
namespace: operation
subset: operations
def: "Query a biological pathways database and retrieve annotation on one or more pathways." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:2265
name: Data retrieval (identifier)
namespace: operation
subset: operations
def: "Query a database and retrieve one or more data identifiers." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2224
name: Data retrieval (ontology concept)
namespace: operation
subset: operations
def: "Query an ontology and retrieve concepts or relations." [http://edamontology.org]
synonym: "Ontology retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2222
name: Data retrieval (ontology annotation)
namespace: operation
subset: operations
def: "Search and retrieve documentation on a bioinformatics ontology." [http://edamontology.org]
synonym: "Ontology information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2468
name: Data retrieval (phylogenetic tree)
namespace: operation
subset: operations
def: "Retrieve a phylogenetic tree from a data resource." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:0257
name: Data retrieval (sequence alignment)
namespace: operation
subset: operations
def: "Display basic information about a sequence alignment." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2473
name: Data retrieval (genotype and phenotype annotation)
namespace: operation
subset: operations
def: "Retrieve information on a specific genotype or phenotype." [http://edamontology.org]
synonym: "Genotype and phenotype information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2472
name: Data retrieval (gene annotation)
namespace: operation
subset: operations
def: "Retrieve information on a specific gene." [http://edamontology.org]
synonym: "Gene information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2471
name: Data retrieval (RNA family annotation)
namespace: operation
subset: operations
def: "Retrieve information on an RNA family." [http://edamontology.org]
synonym: "RNA family information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:2470
name: Data retrieval (protein family annotation)
namespace: operation
subset: operations
def: "Retrieve information on a protein family." [http://edamontology.org]
synonym: "Protein family information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2469
name: Data retrieval (protein interaction annotation)
namespace: operation
subset: operations
def: "Retrieve information on a protein interaction." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:2467
name: Data retrieval (protein annotation)
namespace: operation
subset: operations
def: "Retrieve information on a protein." [http://edamontology.org]
synonym: "Protein information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval

[Term]
id: EDAM_operation:0280
name: Data retrieval (restriction enzyme annotation)
namespace: operation
subset: operations
def: "Retrieve information on restriction enzymes or restriction enzyme sites." [http://edamontology.org]
synonym: "Restriction enzyme information retrieval" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:0515
name: Data retrieval (tool metadata)
namespace: operation
subset: operations
def: "Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function." [http://edamontology.org]
synonym: "Tool information retrieval" EXACT [http://edamontology.org]
synonym: "Data retrieval (tool annotation)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation)
relationship: has_output EDAM_data:0958 {min_cardinality=0} ! Tool metadata


[Term]
id: EDAM_operation:0516
name: Data retrieval (database metadata)
namespace: operation
subset: operations
def: "Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword." [http://edamontology.org]
synonym: "Database information retrieval" EXACT [http://edamontology.org]
synonym: "Data retrieval (database annotation)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation)
relationship: has_output EDAM_data:0957 {min_cardinality=0} ! Database metadata


[Term]
id: EDAM_operation:0344
name: Sequence retrieval (by code)
namespace: operation
subset: operations
def: "Query a database and retrieve sequences with a given entry code or accession number." [http://edamontology.org]
is_a: EDAM_operation:1813 ! Sequence retrieval

[Term]
id: EDAM_operation:0345
name: Sequence retrieval (by keyword)
namespace: operation
subset: operations
def: "Query a database and retrieve sequences containing a given keyword." [http://edamontology.org]
is_a: EDAM_operation:1813 ! Sequence retrieval


[Term]
id: EDAM_operation:1845
name: PDB file sequence retrieval
namespace: operation
subset: operations
def: "Extract a molecular sequence from a PDB file." [http://edamontology.org, WHATIF]
xref: WHATIF: PDB_sequence
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0344 ! Sequence retrieval (by code)

[Term]
id: EDAM_operation:0305
name: Literature search
namespace: operation
subset: operations
def: "Query the biomedical and informatics literature." [http://edamontology.org]
is_a: EDAM_operation:2421 ! Database search
relationship: has_output EDAM_data:0970 {min_cardinality=0} ! Bibliographic reference
relationship: has_topic EDAM_topic:0217 ! Literature analysis

[Term]
id: EDAM_operation:0338
name: Sequence database search
namespace: operation
subset: operations
def: "Search a sequence database by sequence comparison and retrieve similar sequences." [http://edamontology.org]
comment: This excludes direct retrieval methods (e.g. the dbfetch program).
is_a: EDAM_operation:2421 ! Database search
is_a: EDAM_operation:2403 ! Sequence analysis
relationship: has_output EDAM_data:0857 {min_cardinality=0} ! Database hits (sequence)
relationship: has_topic EDAM_topic:0159 ! Sequence comparison


[Term]
id: EDAM_operation:0339
name: Structure database search
namespace: operation
subset: operations
def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org]
is_a: EDAM_operation:2421 ! Database search
is_a: EDAM_operation:2996 ! Structure classification
relationship: has_output EDAM_data:0885 {min_cardinality=0} ! Database hits (structure)
relationship: has_topic EDAM_topic:0081 ! Structure analysis

[Term]
id: EDAM_operation:0340
name: Protein secondary database search
namespace: operation
subset: operations
def: "Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group." [http://edamontology.org]
comment: Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.).
synonym: "Protein sequence classification" EXACT [http://edamontology.org]
is_a: EDAM_operation:2421 ! Database search
is_a: EDAM_operation:3093 ! Sequence screening
relationship: has_output EDAM_data:0858 {min_cardinality=0} ! Database hits (secondary)
relationship: has_topic EDAM_topic:0595 ! Protein classification

[Term]
id: EDAM_operation:0341
name: Motif database search
namespace: operation
subset: operations
def: "Screen a sequence against a motif or pattern database." [http://edamontology.org]
is_a: EDAM_operation:2421 ! Database search
is_a: EDAM_operation:0239 ! Sequence motif recognition
is_a: EDAM_operation:3093 ! Sequence screening
relationship: has_output EDAM_data:1298 {min_cardinality=0} ! Sequence features (motifs)
relationship: has_topic EDAM_topic:0158 ! Sequence motifs

[Term]
id: EDAM_operation:0342
name: Sequence profile database search
namespace: operation
subset: operations
def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org]
is_a: EDAM_operation:2421 ! Database search
is_a: EDAM_operation:0300 ! Sequence-profile alignment construction
is_a: EDAM_operation:3093 ! Sequence screening
relationship: has_output EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_operation:0346
name: Sequence database search (by sequence)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [http://edamontology.org]
synonym: "Sequence similarity search" EXACT [http://edamontology.org]
is_a: EDAM_operation:0338 ! Sequence database search
is_a: EDAM_operation:3093 ! Sequence screening
is_a: EDAM_operation:2451 ! Sequence comparison



[Term]
id: EDAM_operation:0347
name: Sequence database search (by motif or pattern)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [http://edamontology.org]
is_a: EDAM_operation:0338 ! Sequence database search
is_a: EDAM_operation:0239 ! Sequence motif recognition
relationship: has_input EDAM_data:1353 {min_cardinality=1} ! Sequence motif
relationship: has_topic EDAM_topic:0158 ! Sequence motifs


[Term]
id: EDAM_operation:0348
name: Sequence database search (by amino acid composition)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences of a given amino acid composition." [http://edamontology.org]
is_a: EDAM_operation:0338 ! Sequence database search
relationship: has_input EDAM_data:1267 ! Amino acid frequencies
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis


[Term]
id: EDAM_operation:0349
name: Sequence database search (by physicochemical property)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [http://edamontology.org]
is_a: EDAM_operation:0338 ! Sequence database search


[Term]
id: EDAM_operation:0350
name: Sequence database search (by sequence using word-based methods)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method." [http://edamontology.org]
comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.
synonym: "Sequence similarity search (word-based methods)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0346 ! Sequence database search (by sequence)
is_a: EDAM_operation:0288 ! Sequence word comparison

[Term]
id: EDAM_operation:0351
name: Sequence database search (by sequence using profile-based methods)
namespace: operation
subset: operations
def: "Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query." [http://edamontology.org]
comment: This includes tools based on PSI-BLAST.
synonym: "Sequence similarity search (profile-based methods)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0346 ! Sequence database search (by sequence)
is_a: EDAM_operation:0300 ! Sequence-profile alignment construction

[Term]
id: EDAM_operation:0352
name: Sequence database search (by sequence using local alignment-based methods)
namespace: operation
subset: operations
def: "Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method." [http://edamontology.org]
comment: This includes tools based on the Smith-Waterman algorithm or FASTA.
synonym: "Sequence similarity search (local alignment-based methods) " EXACT [http://edamontology.org]
is_a: EDAM_operation:0346 ! Sequence database search (by sequence)
is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local)
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_operation:0353
name: Sequence database search (by sequence using global alignment-based methods)
namespace: operation
subset: operations
def: "Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method." [http://edamontology.org]
comment: This includes tools based on the Needleman and Wunsch algorithm.
synonym: "Sequence similarity search (global alignment-based methods)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0346 ! Sequence database search (by sequence)
is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global)
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_operation:0354
name: Sequence database search (by sequence for primer sequences)
namespace: operation
subset: operations
def: "Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences." [http://edamontology.org]
comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
synonym: "Sequence similarity search (primer sequences)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0346 ! Sequence database search (by sequence)
relationship: has_topic EDAM_topic:3032 ! Primer or probe design

[Term]
id: EDAM_operation:0355
name: Sequence database search (by molecular weight)
namespace: operation
subset: operations
def: "Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry." [http://edamontology.org]
synonym: "Protein fingerprinting" EXACT [http://edamontology.org]
synonym: "Peptide mass fingerprinting" EXACT [http://edamontology.org]
is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property)
relationship: has_input EDAM_data:0944 ! Peptide mass fingerprint
relationship: has_topic EDAM_topic:0123 ! Protein properties
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification


[Term]
id: EDAM_operation:0356
name: Sequence database search (by isoelectric point)
namespace: operation
subset: operations
def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [http://edamontology.org]
is_a: EDAM_operation:0349 ! Sequence database search (by physicochemical property)
relationship: has_topic EDAM_topic:0123 ! Protein properties

[Term]
id: EDAM_operation:0357
name: Structure retrieval (by code)
namespace: operation
subset: operations
def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [http://edamontology.org]
is_a: EDAM_operation:1814 ! Structure retrieval

[Term]
id: EDAM_operation:0358
name: Structure retrieval (by keyword)
namespace: operation
subset: operations
def: "Query a tertiary structure database and retrieve entries containing a given keyword." [http://edamontology.org]
is_a: EDAM_operation:1814 ! Structure retrieval

[Term]
id: EDAM_operation:1914
name: Structure retrieval (water)
namespace: operation
subset: operations
def: "Query a tertiary structure database and retrieve water molecules." [http://edamontology.org]
xref: WHATIF:MovedWaterPDB
is_a: EDAM_operation:1814 ! Structure retrieval


[Term]
id: EDAM_operation:0359
name: Structure database search (by sequence)
namespace: operation
subset: operations
def: "Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence." [http://edamontology.org]
synonym: "Structure retrieval by sequence" EXACT [http://edamontology.org]
is_a: EDAM_operation:0339 ! Structure database search
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:3093 ! Sequence screening

[Term]
id: EDAM_operation:0360
name: Structure database search (by structure)
namespace: operation
subset: operations
def: "Search a tertiary structure database and retrieve structures that are similar to a query structure." [http://edamontology.org]
synonym: "Structure retrieval by structure" EXACT [http://edamontology.org]
synonym: "Structural similarity search" EXACT [http://edamontology.org]
is_a: EDAM_operation:0339 ! Structure database search
relationship: has_topic EDAM_topic:1770 ! Structure comparison
relationship: has_topic EDAM_topic:1770 ! Structure comparison

[Term]
id: EDAM_operation:0226
name: Annotation
namespace: operation
subset: operations
def: "Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary." [http://edamontology.org]
comment: This is a broad concept and is used a placeholder for other, more specific concepts.
is_a: EDAM_operation:0004 ! Operation
relationship: has_input EDAM_data:0582 ! Ontology
relationship: has_topic EDAM_topic:0089 ! Ontology


[Term]
id: EDAM_operation:1774
name: Annotation retrieval
namespace: operation
subset: operations
def: "Retrieve existing annotation (or documentation), typically annotation on a database entity." [http://edamontology.org]
comment: Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:0361
name: Sequence annotation
namespace: operation
subset: operations
def: "Annotate a molecular sequence record with terms from a controlled vocabulary." [http://edamontology.org]
is_a: EDAM_operation:0226 ! Annotation
relationship: has_input EDAM_data:0849 {min_cardinality=1} ! Sequence record
relationship: has_output EDAM_data:0849 {min_cardinality=1} ! Sequence record


[Term]
id: EDAM_operation:0362
name: Genome annotation
namespace: operation
subset: operations
def: "Annotate a genome sequence with terms from a controlled vocabulary." [http://edamontology.org]
is_a: EDAM_operation:0361 ! Sequence annotation


[Term]
id: EDAM_operation:2466
name: Map annotation
namespace: operation
subset: operations
def: "Annotate a DNA map of some type with terms from a controlled vocabulary." [http://edamontology.org]
is_a: EDAM_operation:0226 ! Annotation
is_a: EDAM_operation:2521 ! Map data processing
relationship: has_input EDAM_data:1274 {min_cardinality=1} ! Map
relationship: has_output EDAM_data:1274 {min_cardinality=1} ! Map


[Term]
id: EDAM_operation:0227
name: Data indexing
namespace: operation
subset: operations
def: "Generate an index of (typically a file of) biological data." [http://edamontology.org]
synonym: "Database indexing" EXACT [http://edamontology.org]
is_a: EDAM_operation:2412 ! Data index processing
relationship: has_output EDAM_data:0955 ! Data index


[Term]
id: EDAM_operation:3211 {since=1.1}
name: Genome indexing
namespace: operation
subset: operations
def: "Generate an index of a genome sequence." [http://edamontology.org]
comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
is_a: EDAM_operation:0227 ! Data indexing
relationship: has_output EDAM_data:3210 ! Genome index

[Term]
id: EDAM_operation:3212 {since=1.1}
name: Genome indexing (Burrows-Wheeler)
namespace: operation
subset: operations
def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org]
comment:  The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
synonym: "Burrows-Wheeler" EXACT [http://edamontology.org]
synonym: "Burrows Wheeler" EXACT [http://edamontology.org]
synonym: "Genome indexing (Burrows Wheeler)" EXACT [http://edamontology.org]
is_a: EDAM_operation:3211 ! Genome indexing

[Term]
id: EDAM_operation:3213 {since=1.1}
name: Genome indexing (suffix arrays)
namespace: operation
subset: operations
def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org]
comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome.
synonym: "suffix arrays" EXACT [http://edamontology.org]
is_a: EDAM_operation:3211 ! Genome indexing



[Term]
id: EDAM_operation:0228
name: Data index analysis
namespace: operation
subset: operations
def: "Analyse an index of biological data." [http://edamontology.org]
is_a: EDAM_operation:2412 ! Data index processing
is_a: EDAM_operation:2412 ! Data index processing
synonym: "Database index analysis" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:0955 {min_cardinality=1} ! Data index
relationship: has_output EDAM_data:0956 {min_cardinality=1} ! Data index report


[Term]
id: EDAM_operation:2478
name: Nucleic acid sequence analysis
namespace: operation
subset: operations
def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org]
synonym: "Sequence analysis (nucleic acid)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
relationship: has_input EDAM_data:2977 {min_cardinality=1} ! Nucleic acid sequence
relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:3095 {since=beta13}
name: Nucleic acid design
namespace: operation
subset: operations
def: "Design (or predict) nucleic acid sequences with specific chemical or physical properties." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis





[Term]
id: EDAM_operation:2479
name: Protein sequence analysis
namespace: operation
subset: operations
def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org]
synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2447 ! Sequence processing (protein)
synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:2976 {min_cardinality=1} ! Protein sequence
relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis



[Term]
id: EDAM_operation:3214 {since=1.1}
name: Spectrum analysis
namespace: operation
subset: operations
def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org]
synonym: "Spectral analysis" EXACT [http://edamontology.org]
synonym: "Mass spectrum analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing

[Term]
id: EDAM_operation:3215 {since=1.1}
name: Peak detection
namespace: operation
subset: operations
def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org]
synonym: "Peak finding" EXACT [http://edamontology.org]
is_a: EDAM_operation:3214 ! Spectrum analysis
relationship: has_input EDAM_data:0943 {min_cardinality=1} ! Mass spectrometry spectra


[Term]
id: EDAM_operation:2446
name: Sequence processing
namespace: operation
subset: operations
! alt_id: EDAM_operation:2449
def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org]
synonym: "Sequence processing (general)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0080 ! Sequence analysis

[Term]
id: EDAM_operation:2447
name: Sequence processing (protein)
namespace: operation
subset: operations
def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_input EDAM_data:2976 {min_cardinality=0} ! Protein sequence
relationship: has_output EDAM_data:2976 {min_cardinality=0} ! Protein sequence

[Term]
id: EDAM_operation:2448
name: Sequence processing (nucleic acid)
namespace: operation
subset: operations
def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
is_a: EDAM_operation:2501 ! Nucleic acid data processing
relationship: has_input EDAM_data:2977 {min_cardinality=0} ! Nucleic acid sequence
relationship: has_output EDAM_data:2977 {min_cardinality=0} ! Nucleic acid sequence

[Term]
id: EDAM_operation:0229
name: Annotation retrieval (sequence)
namespace: operation
subset: operations
def: "Retrieve basic information about a molecular sequence." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:1813 ! Sequence retrieval

[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:2513
name: Sequence generation (nucleic acid)
namespace: operation
subset: operations
def: "Generate a nucleic acid sequence by some means." [http://edamontology.org]
is_a: EDAM_operation:0230 ! Sequence generation
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:2514
name: Sequence generation (protein)
namespace: operation
subset: operations
def: "Generate a protein sequence by some means." [http://edamontology.org]
is_a: EDAM_operation:0230 ! Sequence generation
is_a: EDAM_operation:2447 ! Sequence processing (protein)
relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis

[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:2511
name: Sequence editing (nucleic acid)
namespace: operation
subset: operations
def: "Edit or change a nucleic acid sequence, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)

[Term]
id: EDAM_operation:2512
name: Sequence editing (protein)
namespace: operation
subset: operations
def: "Edit or change a protein sequence, either randomly or specifically." [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing
is_a: EDAM_operation:2447 ! Sequence processing (protein)


[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:1780
name: Sequence submission
namespace: operation
subset: operations
def: "Submit a molecular sequence to a database." [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition

[Term]
id: EDAM_operation:0234
name: Sequence complexity calculation
namespace: operation
subset: operations
! alt_id: EDAM_operation:0373
! alt_id: EDAM_operation:0374
def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [http://edamontology.org]
is_a: EDAM_operation:0236 ! Sequence composition calculation
relationship: has_output EDAM_data:1259 {min_cardinality=1} ! Sequence complexity
relationship: has_topic EDAM_topic:0642 ! Low complexity sequences


[Term]
id: EDAM_operation:0235
name: Sequence ambiguity calculation
namespace: operation
subset: operations
! alt_id: EDAM_operation:0375
! alt_id: EDAM_operation:0376
def: "Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes." [http://edamontology.org]
is_a: EDAM_operation:0236 ! Sequence composition calculation
relationship: has_output EDAM_data:1260 {min_cardinality=1} ! Sequence ambiguity
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis


[Term]
id: EDAM_operation:0291
name: Sequence clustering
namespace: operation
subset: operations
def: "Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org]
comment: The clusters may be output or used internally for some other purpose.
synonym: "Sequence cluster generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2452 ! Sequence cluster processing
is_a: EDAM_operation:2995 ! Sequence classification
relationship: has_output EDAM_data:1235 {min_cardinality=0} ! Sequence cluster

[Term]
id: EDAM_operation:0236
name: Sequence composition calculation
namespace: operation
subset: operations
def: "Calculate character or word composition or frequency of a molecular sequence." [http://edamontology.org]
is_a: EDAM_operation:2403 ! Sequence analysis
relationship: has_output EDAM_data:1261 ! Sequence composition
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis


[Term]
id: EDAM_operation:0237
name: Repeat sequence analysis
namespace: operation
subset: operations
def: "Find and/or analyse repeat sequences in (typically nucleotide) sequences." [http://edamontology.org]
comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
is_a: EDAM_operation:2403 ! Sequence analysis
relationship: has_topic EDAM_topic:0641 ! Repeat sequences

[Term]
id: EDAM_operation:0290
name: Sequence redundancy removal
namespace: operation
subset: operations
def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org]
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_output EDAM_data:2044 {min_cardinality=0} ! Sequence
relationship: has_topic EDAM_topic:0164 ! Sequence clustering


[Term]
id: EDAM_operation:2451
name: Sequence comparison
namespace: operation
subset: operations
def: "Compare two or more molecular sequences." [http://edamontology.org]
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:2044 {min_cardinality=2} ! Sequence
relationship: has_output EDAM_data:2955 ! Sequence report
relationship: has_topic EDAM_topic:0159 ! Sequence comparison


[Term]
id: EDAM_operation:2508
name: Nucleic acid sequence comparison
namespace: operation
subset: operations
def: "Compare two or more nucleic acid sequences." [http://edamontology.org]
synonym: "Sequence comparison (nucleic acid)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:2998 ! Nucleic acid comparison

[Term]
id: EDAM_operation:2509
name: Protein sequence comparison
namespace: operation
subset: operations
def: "Compare two or more protein sequences." [http://edamontology.org]
synonym: "Sequence comparison (protein)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2479 ! Protein sequence analysis
is_a: EDAM_operation:2997 ! Protein comparison

[Term]
id: EDAM_operation:0288
name: Sequence word comparison
namespace: operation
subset: operations
def: "Find exact character or word matches between molecular sequences without full sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
relationship: has_output EDAM_data:0861 {min_cardinality=1} ! Sequence alignment (words)

[Term]
id: EDAM_operation:0289
name: Sequence distance matrix generation
namespace: operation
subset: operations
def: "Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences." [http://edamontology.org]
synonym: "Phylogenetic distance matrix generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
relationship: has_output EDAM_data:0870 ! Sequence distance matrix
relationship: has_topic EDAM_topic:0084 ! Phylogenetics

[Term]
id: EDAM_operation:3200 {since=1.1}
name: DNA barcoding
namespace: operation
subset: operations
def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org]
synonym: "Sample barcoding" EXACT [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction



[Term]
id: EDAM_operation:3204 {since=1.1}
name: Methylation analysis
namespace: operation
subset: operations
def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction

[Term]
id: EDAM_operation:3205 {since=1.1}
name: Methylation calling
namespace: operation
subset: operations
def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org]
is_a: EDAM_operation:3204 ! Methylation analysis

[Term]
id: EDAM_operation:3206 {since=1.1}
name: Methylation level analysis (global)
namespace: operation
subset: operations
def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org]
synonym: "Global methylation analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:3205 ! Methylation calling

[Term]
id: EDAM_operation:3207 {since=1.1}
name: Methylation level analysis (gene-specific)
namespace: operation
subset: operations
def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org]
comment: Many different techniques are available for this.
synonym: "Gene-specific methylation analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:3205 ! Methylation calling


[Term]
id: EDAM_operation:3209 {since=1.1}
name: Genome comparison
namespace: operation
subset: operations
! alt_id: EDAM_operation:3193 {since=1.1}
def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org]
synonym: "Genomic region matching" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison


[Term]
id: EDAM_operation:0266
name: Vector sequence detection
namespace: operation
subset: operations
def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction

[Term]
id: EDAM_operation:2233
name: Representative sequence identification
namespace: operation
subset: operations
def: "Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences." [http://edamontology.org]
is_a: EDAM_operation:0291 ! Sequence clustering
relationship: has_topic EDAM_topic:0164 ! Sequence clustering

[Term]
id: EDAM_operation:0317
name: EST and cDNA sequence analysis
namespace: operation
subset: operations
def: "Analyse EST or cDNA sequences." [http://edamontology.org]
comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2403 ! Sequence analysis

[Term]
id: EDAM_operation:3185 {since=1.1}
name: Base-calling
namespace: operation
subset: operations
def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org]
synonym: "Base calling" EXACT [http://edamontology.org]
synonym: "Phred base calling" EXACT [http://edamontology.org]
synonym: "Phred base-calling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
relationship: has_topic EDAM_topic:3168 ! Sequencing


[Term]
id: EDAM_operation:3195
name: Sequencing error detection
namespace: operation
subset: operations
def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org]
synonym: "Short-read error correction" EXACT [http://edamontology.org]
synonym: "Short read error correction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
relationship: has_topic EDAM_topic:3168 ! Sequencing

[Term]
id: EDAM_operation:0265
name: Frameshift error detection
namespace: operation
subset: operations
def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org]
comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
is_a: EDAM_operation:3195 ! Sequencing error detection
is_a: EDAM_operation:3197 ! Genetic variation analysis
relationship: has_topic EDAM_topic:3168 ! Sequencing


[Term]
id: EDAM_operation:0241
name: Transcription regulatory sequence analysis
namespace: operation
subset: operations
def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [http://edamontology.org]
comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0438 ! Transcription regulatory element prediction


[Term]
id: EDAM_operation:0281
name: Genetic marker identification
namespace: operation
subset: operations
def: "Identify genetic markers in DNA sequences." [http://edamontology.org]
comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0415 ! Nucleic acid feature prediction


[Term]
id: EDAM_operation:0363
name: Nucleic acid sequence reverse and complement
namespace: operation
subset: operations
def: "Generate the reverse and / or complement of a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid)

[Term]
id: EDAM_operation:0364
name: Random sequence generation
namespace: operation
subset: operations
def: "Generate a random sequence, for example, with a specific character composition." [http://edamontology.org]
is_a: EDAM_operation:0230 ! Sequence generation

[Term]
id: EDAM_operation:0365
name: Nucleic acid restriction digest
namespace: operation
subset: operations
def: "Generate digest fragments for a nucleotide sequence containing restriction sites." [http://edamontology.org]
is_a: EDAM_operation:2513 ! Sequence generation (nucleic acid)
is_a: EDAM_operation:0262 ! Nucleic acid property calculation
relationship: has_output EDAM_data:1239 ! Restriction digest
relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction


[Term]
id: EDAM_operation:0366
name: Protein sequence cleavage
namespace: operation
subset: operations
def: "Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses." [http://edamontology.org]
is_a: EDAM_operation:2514 ! Sequence generation (protein)
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1238 ! Proteolytic digest
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

[Term]
id: EDAM_operation:0367
name: Sequence mutation and randomization
namespace: operation
subset: operations
def: "Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition." [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing

[Term]
id: EDAM_operation:0368
name: Sequence masking
namespace: operation
subset: operations
def: "Mask characters in a molecular sequence (replacing those characters with a mask character)." [http://edamontology.org]
comment: For example, SNPs or repeats in a DNA sequence might be masked.
is_a: EDAM_operation:0231 ! Sequence editing
relationship: has_input EDAM_data:0851 {min_cardinality=1} ! Sequence mask character

[Term]
id: EDAM_operation:0369
name: Sequence cutting
namespace: operation
subset: operations
def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org]
is_a: EDAM_operation:0231 ! Sequence editing

[Term]
id: EDAM_operation:3192 {since=1.1}
name: Sequence trimming
namespace: operation
subset: operations
def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org]
is_a: EDAM_operation:0369 ! Sequence cutting


[Term]
id: EDAM_operation:3212 {since=1.1}
name: Primer removal
namespace: operation
subset: operations
def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org]
is_a: EDAM_operation:0369 ! Sequence cutting
is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid)


[Term]
id: EDAM_operation:3189 {since=1.1}
name: Trim ends
namespace: operation
subset: operations
def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org]
comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
is_a: EDAM_operation:3192 ! Sequence trimming

[Term]
id: EDAM_operation:3190 {since=1.1}
name: Trim vector
namespace: operation
subset: operations
def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org]
is_a: EDAM_operation:3192 ! Sequence trimming

[Term]
id: EDAM_operation:3191 {since=1.1}
name: Trim to reference
namespace: operation
subset: operations
def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org]
is_a: EDAM_operation:3192 ! Sequence trimming



[Term]
id: EDAM_operation:0370
name: Restriction site creation
namespace: operation
subset: operations
def: "Create (or remove) restriction sites in sequences, for example using silent mutations." [http://edamontology.org]
is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid)
relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction

[Term]
id: EDAM_operation:0371
name: DNA translation
namespace: operation
subset: operations
def: "Translate a DNA sequence into protein." [http://edamontology.org]
is_a: EDAM_operation:0233 ! Sequence conversion
relationship: has_topic EDAM_topic:0108 ! Translation


[Term]
id: EDAM_operation:0372
name: DNA transcription
namespace: operation
subset: operations
def: "Transcribe a nucleotide sequence into mRNA sequence(s)." [http://edamontology.org]
is_a: EDAM_operation:0233 ! Sequence conversion
relationship: has_topic EDAM_topic:0110 ! Transcription


[Term]
id: EDAM_operation:2510
name: DNA back-translation
namespace: operation
subset: operations
def: "Back-translate a protein sequence into DNA." [http://edamontology.org]
is_a: EDAM_operation:0233 ! Sequence conversion
relationship: has_topic EDAM_topic:0108 ! Translation


[Term]
id: EDAM_operation:0377
name: Sequence composition calculation (nucleic acid)
namespace: operation
subset: operations
def: "Calculate base frequency or word composition of a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_operation:0236 ! Sequence composition calculation
is_a: EDAM_operation:0262 ! Nucleic acid property calculation


[Term]
id: EDAM_operation:0378
name: Sequence composition calculation (protein)
namespace: operation
subset: operations
def: "Calculate amino acid frequency or word composition of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0236 ! Sequence composition calculation
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)

[Term]
id: EDAM_operation:2284
name: Nucleic acid density plotting
namespace: operation
subset: operations
def: "Calculate a density plot (of base composition) for a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_operation:0377 ! Sequence composition calculation (nucleic acid)

[Term]
id: EDAM_operation:0379
name: Repeat sequence detection
namespace: operation
subset: operations
! alt_id: EDAM_operation:2450
def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org]
is_a: EDAM_operation:0237 ! Repeat sequence analysis
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1299 ! Sequence features (repeats)


[Term]
id: EDAM_operation:0380
name: Repeat sequence organisation analysis
namespace: operation
subset: operations
def: "Analyse repeat sequence organization such as periodicity." [http://edamontology.org]
is_a: EDAM_operation:0237 ! Repeat sequence analysis
is_a: EDAM_operation:0236 ! Sequence composition calculation


[Term]
id: EDAM_operation:0490
name: Dotplot plotting
namespace: operation
subset: operations
def: "Draw a dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org]
is_a: EDAM_operation:0288 ! Sequence word comparison
is_a: EDAM_operation:0565 ! Sequence alignment rendering
relationship: has_output EDAM_data:0862 {min_cardinality=1} ! Dotplot

[Term]
id: EDAM_operation:0242
name: Conserved transcription regulatory sequence identification
namespace: operation
subset: operations
def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org]
comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1315 ! Gene features (TFBS)

[Term]
id: EDAM_operation:0238
name: Sequence motif discovery
namespace: operation
subset: operations
def: "Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery)." [http://edamontology.org]
comment: Motifs and patterns might be conserved or over-represented (occur with improbable frequency).
synonym: "Motif discovery" EXACT [http://edamontology.org]
is_a: EDAM_operation:0253 ! Feature prediction
is_a: EDAM_operation:2404 ! Sequence motif processing
relationship: has_output EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_operation:0239
name: Sequence motif recognition
namespace: operation
subset: operations
def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org]
synonym: "Sequence motif detection" EXACT [http://edamontology.org]
synonym: "Motif detection" EXACT [http://edamontology.org]
synonym: "Motif recognition" EXACT [http://edamontology.org]
is_a: EDAM_operation:2404 ! Sequence motif processing
is_a: EDAM_operation:0253 ! Feature prediction
relationship: has_output EDAM_data:1298 ! Sequence features (motifs)


[Term]
id: EDAM_operation:0240
name: Sequence motif comparison
namespace: operation
subset: operations
def: "Find motifs shared by molecular sequences." [http://edamontology.org]
is_a: EDAM_operation:2451 ! Sequence comparison
is_a: EDAM_operation:2404 ! Sequence motif processing
relationship: has_output EDAM_data:1298 ! Sequence features (motifs)



[Term]
id: EDAM_operation:2123
name: Small molecule data processing
namespace: operation
subset: operations
def: "Process (read and / or write) physicochemical property data for small molecules." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2420 ! Analysis and processing


[Term]
id: EDAM_operation:0250
name: Protein property calculation
namespace: operation
subset: operations
! alt_id: EDAM_operation:2933
def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org]
comment: This includes methods to render and visualise the properties of a protein sequence.
synonym: "Protein property rendering" EXACT [http://edamontology.org]
is_a: EDAM_operation:2502 ! Protein data processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_input EDAM_data:0897 {min_cardinality=0} ! Protein property
relationship: has_output EDAM_data:0897 {min_cardinality=0} ! Protein property
relationship: has_topic EDAM_topic:0123 ! Protein properties

[Term]
id: EDAM_operation:3088 {since=beta13}
name: Protein property calculation (from sequence)
namespace: operation
subset: operations
def: "Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0250 ! Protein property calculation
is_a: EDAM_operation:2479 ! Protein sequence analysis



[Term]
id: EDAM_operation:0261
name: Nucleic acid property processing
namespace: operation
subset: operations
def: "Process (read and / or write) physicochemical property data of nucleic acids." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0262 ! Nucleic acid property calculation


[Term]
id: EDAM_operation:0334
name: Enzyme kinetics calculation
namespace: operation
subset: operations
def: "Calculate Km, Vmax and derived data for an enzyme reaction." [http://edamontology.org]
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:2024 {min_cardinality=1} ! Enzyme kinetics data
relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions

[Term]
id: EDAM_operation:0398
name: Protein molecular weight calculation
namespace: operation
subset: operations
def: "Calculate the molecular weight of a protein sequence or fragments." [http://edamontology.org]
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1519 {min_cardinality=1} ! Peptide molecular weights
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification


[Term]
id: EDAM_operation:2930
name: Protein property comparison
namespace: operation
subset: operations
def: "Compare the physicochemical properties of two or more proteins (or reference data)." [http://edamontology.org]
is_a: EDAM_operation:2997 ! Protein comparison
relationship: has_output EDAM_data:0897 {min_cardinality=1} ! Protein property


[Term]
id: EDAM_operation:2929
name: Protein fragment weight comparison
namespace: operation
subset: operations
def: "Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data." [http://edamontology.org]
is_a: EDAM_operation:0398 ! Protein molecular weight calculation
is_a: EDAM_operation:2930 ! Protein property comparison

[Term]
id: EDAM_operation:0399
name: Protein extinction coefficient calculation
namespace: operation
subset: operations
def: "Predict extinction coefficients or optical density of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1531 {min_cardinality=1} ! Protein extinction coefficient


[Term]
id: EDAM_operation:0400
name: Protein pH-dependent property calculation
namespace: operation
subset: operations
def: "Calculate pH-dependent properties from pKa calculations of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:0897 ! Protein property
relationship: has_topic EDAM_topic:0137 ! Protein hydropathy

[Term]
id: EDAM_operation:0401
name: Protein hydropathy calculation (from sequence)
namespace: operation
subset: operations
def: "Hydropathy calculation on a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:2574 ! Protein hydropathy calculation

[Term]
id: EDAM_operation:0252
name: Peptide immunogenicity prediction
namespace: operation
subset: operations
def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins." [http://edamontology.org]
comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
is_a: EDAM_operation:2492 ! Protein interaction prediction
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1534 {min_cardinality=1} ! Peptide immunogenicity data
relationship: has_topic EDAM_topic:0804 ! Immunoinformatics


[Term]
id: EDAM_operation:2932
name: Hopp and Woods plotting
namespace: operation
subset: operations
def: "Generate a Hopp and Woods plot of antigenicity of a protein." [http://edamontology.org]
is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction


[Term]
id: EDAM_operation:0402
name: Protein titration curve plotting
namespace: operation
subset: operations
def: "Plot a protein titration curve." [http://edamontology.org]
is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation
relationship: has_output EDAM_data:1527 {min_cardinality=1} ! Protein titration curve


[Term]
id: EDAM_operation:0403
name: Protein isoelectric point calculation
namespace: operation
subset: operations
def: "Calculate isoelectric point of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation
relationship: has_output EDAM_data:1528 {min_cardinality=1} ! Protein isoelectric point


[Term]
id: EDAM_operation:0404
name: Protein hydrogen exchange rate calculation
namespace: operation
subset: operations
def: "Estimate hydrogen exchange rate of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0400 ! Protein pH-dependent property calculation
relationship: has_output EDAM_data:1530 {min_cardinality=1} ! Protein hydrogen exchange rate

[Term]
id: EDAM_operation:0405
name: Protein hydrophobic region calculation
namespace: operation
subset: operations
def: "Calculate hydrophobic or hydrophilic / charged regions of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)

[Term]
id: EDAM_operation:0406
name: Protein aliphatic index calculation
namespace: operation
subset: operations
def: "Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein." [http://edamontology.org]
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)
relationship: has_output EDAM_data:1521 {min_cardinality=1} ! Protein aliphatic index

[Term]
id: EDAM_operation:0407
name: Protein hydrophobic moment plotting
namespace: operation
subset: operations
def: "Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity." [http://edamontology.org]
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)
relationship: has_output EDAM_data:1520 {min_cardinality=1} ! Peptide hydrophobic moment

[Term]
id: EDAM_operation:0408
name: Protein globularity prediction
namespace: operation
subset: operations
def: "Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc." [http://edamontology.org]
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)
relationship: has_output EDAM_data:1526 {min_cardinality=1} ! Protein globularity

[Term]
id: EDAM_operation:0409
name: Protein solubility prediction
namespace: operation
subset: operations
def: "Predict the solubility or atomic solvation energy of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)
relationship: has_output EDAM_data:1524 {min_cardinality=1} ! Protein solubility

[Term]
id: EDAM_operation:0410
name: Protein crystallizability prediction
namespace: operation
subset: operations
def: "Predict crystallizability of a protein sequence." [http://edamontology.org]
is_a: EDAM_operation:0401 ! Protein hydropathy calculation (from sequence)
relationship: has_output EDAM_data:1525 {min_cardinality=1} ! Protein crystallizability


[Term]
id: EDAM_operation:0455
name: Nucleic acid thermodynamic property calculation
namespace: operation
subset: operations
def: "Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy." [http://edamontology.org]
is_a: EDAM_operation:0262 ! Nucleic acid property calculation
relationship: has_output EDAM_data:2985 {min_cardinality=1} ! Nucleic acid thermodynamic data



[Term]
id: EDAM_operation:0456
name: Nucleic acid melting profile plotting
namespace: operation
subset: operations
def: "Calculate and plot a DNA or DNA/RNA melting profile." [http://edamontology.org]
comment: A melting profile is used to visualise and analyse partly melted DNA conformations.
is_a: EDAM_operation:0262 ! Nucleic acid property calculation
relationship: has_output EDAM_data:1583 {min_cardinality=1} ! Nucleic acid melting profile


[Term]
id: EDAM_operation:0262
name: Nucleic acid property calculation
namespace: operation
subset: operations
def: "Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_output EDAM_data:0912 {min_cardinality=1} ! Nucleic acid property



[Term]
id: EDAM_operation:2439
name: RNA secondary structure processing
namespace: operation
subset: operations
def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org]
is_a: EDAM_operation:2482 ! Secondary structure processing
is_a: EDAM_operation:2501 ! Nucleic acid data processing
relationship: has_input EDAM_data:0880 {min_cardinality=0} ! RNA secondary structure record
relationship: has_output EDAM_data:0880 {min_cardinality=0} ! RNA secondary structure record
relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis
relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment


[Term]
id: EDAM_operation:2519
name: Structure processing (nucleic acid)
namespace: operation
subset: operations
def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org]
is_a: EDAM_operation:2465 ! Structure processing
is_a: EDAM_operation:2501 ! Nucleic acid data processing
relationship: has_input EDAM_data:1459 {min_cardinality=0} ! Nucleic acid structure
relationship: has_output EDAM_data:1459 {min_cardinality=0} ! Nucleic acid structure
relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis


[Term]
id: EDAM_operation:2440
name: Structure processing (RNA)
namespace: operation
subset: operations
def: "Process (read and / or write) RNA tertiary structure data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2519 ! Structure processing (nucleic acid)



[Term]
id: EDAM_operation:0278
name: RNA secondary structure prediction
namespace: operation
subset: operations
def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org]
comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
is_a: EDAM_operation:2439 ! RNA secondary structure processing
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:0880 {min_cardinality=1} ! RNA secondary structure record
relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction

[Term]
id: EDAM_operation:2441
name: RNA structure prediction
namespace: operation
subset: operations
def: "Predict RNA tertiary structure." [http://edamontology.org]
is_a: EDAM_operation:0475 ! Nucleic acid structure prediction
relationship: has_output EDAM_data:1465 {min_cardinality=1} ! RNA structure record


[Term]
id: EDAM_operation:2442
name: DNA structure prediction
namespace: operation
subset: operations
def: "Predict DNA tertiary structure." [http://edamontology.org]
is_a: EDAM_operation:0475 ! Nucleic acid structure prediction
relationship: has_output EDAM_data:1464 {min_cardinality=1} ! DNA structure

[Term]
id: EDAM_operation:0279
name: Nucleic acid folding analysis
namespace: operation
subset: operations
def: "Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data." [http://edamontology.org]
is_a: EDAM_operation:2426 ! Modelling and simulation
is_a: EDAM_operation:2501 ! Nucleic acid data processing
synonym: "Nucleic acid folding" EXACT [http://edamontology.org]
synonym: "Nucleic acid folding modelling" EXACT [http://edamontology.org]
relationship: has_output EDAM_data:1596 ! Nucleic acid folding report
relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction


[Term]
id: EDAM_operation:0461
name: Nucleic acid curvature calculation
namespace: operation
subset: operations
def: "Calculate curvature and flexibility / stiffness of a nucleotide sequence." [http://edamontology.org]
comment: This includes properties such as.
is_a: EDAM_operation:0262 ! Nucleic acid property calculation
relationship: has_output EDAM_data:0912 {min_cardinality=1} ! Nucleic acid property
relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis

[Term]
id: EDAM_operation:1768
name: Nucleic acid folding family identification
namespace: operation
subset: operations
def: "Identify folding families of related RNAs." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0483 ! Structured RNA prediction and optimisation

[Term]
id: EDAM_operation:1769
name: Nucleic acid folding energy calculation
namespace: operation
subset: operations
def: "Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants." [http://edamontology.org]
is_a: EDAM_operation:0279 ! Nucleic acid folding analysis


[Term]
id: EDAM_operation:1777
name: Protein function prediction
namespace: operation
subset: operations
def: "Predict general functional properties of a protein." [http://edamontology.org]
comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
is_a: EDAM_operation:2414 ! Protein function analysis
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_topic EDAM_topic:2276 ! Protein function prediction


[Term]
id: EDAM_operation:3084 {since=beta13}
name: Protein function prediction (from sequence)
namespace: operation
subset: operations
def: "Predict general (non-positional) functional properties of a protein from analysing its sequence." [http://edamontology.org]
comment: For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
is_a: EDAM_operation:1777 ! Protein function prediction
is_a: EDAM_operation:2479 ! Protein sequence analysis
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_topic EDAM_topic:2276 ! Protein function prediction



[Term]
id: EDAM_operation:1778
name: Protein function comparison
namespace: operation
subset: operations
def: "Compare the functional properties of two or more proteins." [http://edamontology.org]
is_a: EDAM_operation:2414 ! Protein function analysis
is_a: EDAM_operation:2997 ! Protein comparison
relationship: has_topic EDAM_topic:1775 ! Protein function analysis

[Term]
id: EDAM_operation:0413
name: MHC peptide immunogenicity prediction
namespace: operation
subset: operations
def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [http://edamontology.org]
is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction

[Term]
id: EDAM_operation:0253
name: Feature prediction
namespace: operation
subset: operations
def: "Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions." [http://edamontology.org]
synonym: "Sequence feature detection" EXACT [http://edamontology.org]
synonym: "sequence_feature" RELATED [SO:0000110]
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2423 ! Prediction, detection and recognition
relationship: has_output EDAM_data:1255 {min_cardinality=1} ! Feature record
relationship: has_topic EDAM_topic:3072 ! Sequence feature detection


[Term]
id: EDAM_operation:2453
name: Feature table processing
namespace: operation
subset: operations
def: "Process (read and / or write) a sequence feature table." [http://edamontology.org]
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:1270 {min_cardinality=0} ! Sequence feature table
relationship: has_input EDAM_data:2201 {min_cardinality=0} ! Sequence record full
relationship: has_output EDAM_data:1255 {min_cardinality=0} ! Feature record
relationship: has_topic EDAM_topic:0160 ! Sequence sites and features

[Term]
id: EDAM_operation:0254
name: Data retrieval (feature table)
namespace: operation
subset: operations
def: "Extract a sequence feature table from a sequence database entry." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:2422 ! Data retrieval


[Term]
id: EDAM_operation:0255
name: Feature table query
namespace: operation
subset: operations
def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org]
is_a: EDAM_operation:2453 ! Feature table processing
relationship: has_input EDAM_data:1270 {min_cardinality=0} ! Sequence feature table
relationship: has_input EDAM_data:2201 {min_cardinality=0} ! Sequence record full
relationship: has_output EDAM_data:1255 ! Feature record

[Term]
id: EDAM_operation:0256
name: Feature comparison
namespace: operation
subset: operations
def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org]
synonym: "Feature table comparison" EXACT [http://edamontology.org]
synonym: "Sequence feature comparison" EXACT [http://edamontology.org]
is_a: EDAM_operation:2453 ! Feature table processing
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:1270 {min_cardinality=0} ! Sequence feature table
relationship: has_input EDAM_data:2201 {min_cardinality=0} ! Sequence record full



[Term]
id: EDAM_operation:3092 {since=beta13}
name: Protein feature prediction
namespace: operation
subset: operations
def: "Predict, recognise and identify positional features in proteins from analysing protein sequences or structures." [http://edamontology.org]
is_a: EDAM_operation:2502 ! Protein data processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
is_a: EDAM_operation:0253 ! Feature prediction
relationship: has_output EDAM_data:1277 {min_cardinality=1} ! Protein features
relationship: has_topic EDAM_topic:3074 ! Protein feature detection



[Term]
id: EDAM_operation:0414
name: Protein feature prediction (from sequence)
namespace: operation
subset: operations
def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org]
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
synonym: "Sequence feature detection (protein)" EXACT [http://edamontology.org]
is_a: EDAM_operation:3092 ! Protein feature prediction
! is_a: EDAM_operation:0253 ! Feature prediction
is_a: EDAM_operation:2479 ! Protein sequence analysis



[Term]
id: EDAM_operation:3090 {since=beta13}
name: Protein feature prediction (from structure)
namespace: operation
subset: operations
def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org]
is_a: EDAM_operation:3092 ! Protein feature prediction
is_a: EDAM_operation:2406 ! Protein structure analysis




[Term]
id: EDAM_operation:3087 {since=beta13}
name: Protein site detection
namespace: operation
subset: operations
! alt_id: EDAM_operation:0382
def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org]
synonym: "name: Sequence motif recognition (protein)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence)
is_a: EDAM_operation:0239 ! Sequence motif recognition




[Term]
id: EDAM_operation:0415
name: Nucleic acid feature prediction
namespace: operation
subset: operations
! alt_id: EDAM_operation:0381
def: "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org]
comment: Methods typically involve scanning for known motifs, patterns and regular expressions.
synonym: "Sequence feature detection (nucleic acid)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0239 ! Sequence motif recognition
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
is_a: EDAM_operation:0253 ! Feature prediction
relationship: has_output EDAM_data:1276 {min_cardinality=1} ! Nucleic acid features
relationship: has_topic EDAM_topic:3073 ! Nucleic acid feature detection









[Term]
id: EDAM_operation:0416
name: Epitope mapping
namespace: operation
subset: operations
def: "Predict antigenic determinant sites (epitopes) in protein sequences." [http://edamontology.org]
comment: Epitope mapping is commonly done during vaccine design.
is_a: EDAM_operation:3087 ! Protein site detection
is_a: EDAM_operation:2429 ! Mapping and assembly
relationship: has_output EDAM_data:1326 ! Protein features (binding sites)
relationship: has_topic EDAM_topic:0804 ! Immunoinformatics

[Term]
id: EDAM_operation:0417
name: Protein post-translation modification site prediction
namespace: operation
subset: operations
def: "Predict post-translation modification sites in protein sequences." [http://edamontology.org]
comment: Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.
is_a: EDAM_operation:3087 ! Protein site detection
relationship: has_output EDAM_data:1324 ! Protein features (post-translation modifications)
relationship: has_topic EDAM_topic:0601 ! Protein modifications

[Term]
id: EDAM_operation:2489
name: Protein subcellular localization prediction
namespace: operation
subset: operations
def: "Predict the subcellular localization of a protein sequence." [http://edamontology.org]
comment: The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
synonym: "Protein targeting prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:3084 ! Protein function prediction (from sequence)
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization

[Term]
id: EDAM_operation:0418
name: Protein signal peptide detection
namespace: operation
subset: operations
def: "Detect or predict signal peptides and signal peptide cleavage sites in protein sequences." [http://edamontology.org]
comment: Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
is_a: EDAM_operation:3087 ! Protein site detection
is_a: EDAM_operation:2489 ! Protein subcellular localization prediction
relationship: has_output EDAM_data:1322 ! Protein features (signal peptides)
relationship: has_topic EDAM_topic:0140 ! Protein targeting and localization


[Term]
id: EDAM_operation:0419
name: Binding site prediction (from sequence)
namespace: operation
subset: operations
def: "Predict catalytic residues, active sites or other ligand-binding sites in protein sequences." [http://edamontology.org]
synonym: "Ligand-binding and active site prediction (from sequence)" EXACT [http://edamontology.org]
is_a: EDAM_operation:3087 ! Protein site detection
is_a: EDAM_operation:2575 ! Binding site prediction


[Term]
id: EDAM_operation:0420
name: Protein-nucleic acid binding prediction
namespace: operation
subset: operations
def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0419 ! Binding site prediction (from sequence)
relationship: has_output EDAM_data:1326 {min_cardinality=0} ! Protein features (binding sites)

[Term]
id: EDAM_operation:0421
name: Protein folding site prediction
namespace: operation
subset: operations
def: "Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization." [http://edamontology.org]
is_a: EDAM_operation:3087 ! Protein site detection
is_a: EDAM_operation:2415 ! Protein folding analysis
relationship: has_output EDAM_data:2989 {min_cardinality=1} ! Protein features (key folding sites)

[Term]
id: EDAM_operation:0422
name: Protein cleavage site prediction
namespace: operation
subset: operations
def: "Detect or predict cleavage sites (enzymatic or chemical) in protein sequences." [http://edamontology.org]
is_a: EDAM_operation:3087 ! Protein site detection
relationship: has_output EDAM_data:1323 ! Protein features (cleavage sites)
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

[Term]
id: EDAM_operation:0423
name: Epitope mapping (MHC Class I)
namespace: operation
subset: operations
def: "Predict epitopes that bind to MHC class I molecules." [http://edamontology.org]
is_a: EDAM_operation:0416 ! Epitope mapping


[Term]
id: EDAM_operation:0424
name: Epitope mapping (MHC Class II)
namespace: operation
subset: operations
def: "Predict epitopes that bind to MHC class II molecules." [http://edamontology.org]
is_a: EDAM_operation:0416 ! Epitope mapping

[Term]
id: EDAM_operation:0411
name: Protein signal peptide detection (eukaryotes)
namespace: operation
subset: operations
def: "Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins." [http://edamontology.org]
is_a: EDAM_operation:0418 ! Protein signal peptide detection


[Term]
id: EDAM_operation:0412
name: Protein signal peptide detection (bacteria)
namespace: operation
subset: operations
def: "Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins." [http://edamontology.org]
is_a: EDAM_operation:0418 ! Protein signal peptide detection




[Term]
id: EDAM_operation:3222 {since=1.1}
name: Peak calling
namespace: operation
subset: operations
def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org]
comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence.  The enriched areas contain the binding sites of DNA-associated proteins.  For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). 
synonym: "Protein binding peak detection" EXACT [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction



[Term]
id: EDAM_operation:2454
name: Gene and gene component prediction
namespace: operation
subset: operations
def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org]
synonym: "Gene finding" EXACT [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)
relationship: has_topic EDAM_topic:0109 ! Gene finding




[Term]
id: EDAM_operation:0425
name: Whole gene prediction
namespace: operation
subset: operations
def: "Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc." [http://edamontology.org]
is_a: EDAM_operation:2454 ! Gene and gene component prediction


[Term]
id: EDAM_operation:0426
name: Gene component prediction
namespace: operation
subset: operations
def: "Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences." [http://edamontology.org]
comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
is_a: EDAM_operation:2454 ! Gene and gene component prediction


[Term]
id: EDAM_operation:0427
name: Transposon prediction
namespace: operation
subset: operations
def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements)

[Term]
id: EDAM_operation:0428
name: PolyA signal detection
namespace: operation
subset: operations
def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site)

[Term]
id: EDAM_operation:0429
name: Quadruplex formation site detection
namespace: operation
subset: operations
! alt_id: EDAM_operation:2455
def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org]
comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
synonym: "Quadruplex structure prediction" EXACT [http://edamontology.org]
relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes)
relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction

[Term]
id: EDAM_operation:0430
name: CpG island and isochore detection
namespace: operation
subset: operations
! alt_id: EDAM_operation:0576
def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequences." [http://edamontology.org]
comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.
synonym: "CpG island and isochores detection" EXACT [http://edamontology.org]
synonym: "CpG island and isochores rendering" EXACT [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore)
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis


[Term]
id: EDAM_operation:0431
name: Restriction site recognition
namespace: operation
subset: operations
def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites)
relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction

[Term]
id: EDAM_operation:0433
name: Splice site prediction
namespace: operation
subset: operations
def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org]
comment: Methods might require a pre-mRNA or genomic DNA sequence.
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_operation:0453
name: Nucleosome formation potential prediction
namespace: operation
subset: operations
def: "Predict nucleosome formation potential of DNA sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0432 ! Nucleosome formation or exclusion sequence prediction

[Term]
id: EDAM_operation:0432
name: Nucleosome formation or exclusion sequence prediction
namespace: operation
subset: operations
def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org]
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences)


[Term]
id: EDAM_operation:0434
name: Integrated gene prediction
namespace: operation
subset: operations
def: "Predict whole gene structure using a combination of multiple methods to achieve better predictions." [http://edamontology.org]
is_a: EDAM_operation:0425 ! Whole gene prediction


[Term]
id: EDAM_operation:0435
name: Operon prediction
namespace: operation
subset: operations
def: "Find operons (operators, promoters and genes) in bacteria genes." [http://edamontology.org]
is_a: EDAM_operation:0425 ! Whole gene prediction


[Term]
id: EDAM_operation:0464
name: tRNA gene prediction
namespace: operation
subset: operations
def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [http://edamontology.org]
is_a: EDAM_operation:0425 ! Whole gene prediction
relationship: has_topic EDAM_topic:0663 ! tRNA

[Term]
id: EDAM_operation:0436
name: Coding region prediction
namespace: operation
subset: operations
def: "Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences." [http://edamontology.org]
is_a: EDAM_operation:0426 ! Gene component prediction
relationship: has_output EDAM_data:1313 ! Nucleic acid features (coding sequence)


[Term]
id: EDAM_operation:0437
name: Selenocysteine insertion sequence (SECIS) prediction
namespace: operation
subset: operations
def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org]
comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.
is_a: EDAM_operation:0426 ! Gene component prediction
relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)

[Term]
id: EDAM_operation:0438
name: Transcription regulatory element prediction
namespace: operation
subset: operations
def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [http://edamontology.org]
comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
is_a: EDAM_operation:0426 ! Gene component prediction
relationship: has_topic EDAM_topic:0110 ! Transcription
relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites


[Term]
id: EDAM_operation:0439
name: Translation initiation site prediction
namespace: operation
subset: operations
def: "Predict translation initiation sites, possibly by searching a database of sites." [http://edamontology.org]
is_a: EDAM_operation:0436 ! Coding region prediction
relationship: has_topic EDAM_topic:0108 ! Translation

[Term]
id: EDAM_operation:0440
name: Promoter prediction
namespace: operation
subset: operations
def: "Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences." [http://edamontology.org]
comment: Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction
relationship: has_output EDAM_data:1312 ! Gene features (promoter)

[Term]
id: EDAM_operation:0441
name: Transcription regulatory element prediction (DNA-cis)
namespace: operation
subset: operations
def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [http://edamontology.org]
comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction


[Term]
id: EDAM_operation:0442
name: Transcription regulatory element prediction (RNA-cis)
namespace: operation
subset: operations
def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [http://edamontology.org]
comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction


[Term]
id: EDAM_operation:0443
name: Transcription regulatory element prediction (trans)
namespace: operation
subset: operations
def: "Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets." [http://edamontology.org]
comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
synonym: "Functional RNA identification" EXACT [http://edamontology.org]
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction
relationship: has_topic EDAM_topic:3060 ! Regulatory RNA


[Term]
id: EDAM_operation:0444
name: Matrix/scaffold attachment site prediction
namespace: operation
subset: operations
def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [http://edamontology.org]
comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
is_a: EDAM_operation:0438 ! Transcription regulatory element prediction
relationship: has_output EDAM_data:1308 ! Nucleic acid features (matrix/scaffold attachment sites)

[Term]
id: EDAM_operation:0445
name: Transcription factor binding site prediction
namespace: operation
subset: operations
def: "Identify or predict transcription factor binding sites in DNA sequences." [http://edamontology.org]
is_a: EDAM_operation:0440 ! Promoter prediction
relationship: has_output EDAM_data:1315 ! Gene features (TFBS)


[Term]
id: EDAM_operation:0446
name: Exonic splicing enhancer prediction
namespace: operation
subset: operations
def: "Identify or predict exonic splicing enhancers (ESE) in exons." [http://edamontology.org]
comment: An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.
is_a: EDAM_operation:0440 ! Promoter prediction
relationship: has_output EDAM_data:2397 ! Nucleic acid features (exon)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_operation:2008
name: siRNA duplex prediction
namespace: operation
subset: operations
def: "Identify or predict siRNA duplexes in RNA." [http://edamontology.org]
is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans)
relationship: has_output EDAM_data:2169 ! Nucleic acid features (siRNA)
relationship: has_topic EDAM_topic:3060 ! Regulatory RNA


[Term]
id: EDAM_operation:0465
name: siRNA binding specificity prediction
namespace: operation
subset: operations
def: "Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences." [http://edamontology.org]
is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans)
relationship: has_topic EDAM_topic:3060 ! Regulatory RNA


[Term]
id: EDAM_operation:0463
name: microRNA detection
namespace: operation
subset: operations
def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [http://edamontology.org]
is_a: EDAM_operation:0443 ! Transcription regulatory element prediction (trans)
relationship: has_output EDAM_data:1310 ! Nucleic acid features (microRNA)



[Term]
id: EDAM_operation:0259
name: Sequence alignment comparison
namespace: operation
subset: operations
def: "Compare (typically by aligning) two molecular sequence alignments." [http://edamontology.org]
comment: See also 'Sequence profile alignment'.
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2424 ! Comparison

[Term]
id: EDAM_operation:0260
name: Sequence alignment conversion
namespace: operation
subset: operations
def: "Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence)." [http://edamontology.org]
is_a: EDAM_operation:3081 ! Sequence alignment editing


[Term]
id: EDAM_operation:0447
name: Sequence alignment quality evaluation
namespace: operation
subset: operations
def: "Evaluate molecular sequence alignment accuracy." [http://edamontology.org]
comment: Evaluation might be purely sequence-based or use structural information.
is_a: EDAM_operation:2428 ! Evaluation and validation
is_a: EDAM_operation:0258 ! Sequence alignment analysis

[Term]
id: EDAM_operation:0448
name: Sequence alignment analysis (conservation)
namespace: operation
subset: operations
def: "Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence." [http://edamontology.org]
comment: Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.
is_a: EDAM_operation:0258 ! Sequence alignment analysis
relationship: has_output EDAM_data:1415 ! Sequence alignment report (site conservation)

[Term]
id: EDAM_operation:0449
name: Sequence alignment analysis (site correlation)
namespace: operation
subset: operations
def: "Analyse correlations between sites in a molecular sequence alignment." [http://edamontology.org]
comment: This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
is_a: EDAM_operation:0258 ! Sequence alignment analysis
relationship: has_output EDAM_data:1416 ! Sequence alignment report (site correlation)

[Term]
id: EDAM_operation:0450
name: Sequence alignment analysis (chimeric sequence detection)
namespace: operation
subset: operations
def: "Detects chimeric sequences (chimeras) from a sequence alignment." [http://edamontology.org]
comment: A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.
is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid)
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis


[Term]
id: EDAM_operation:0451
name: Sequence alignment analysis (recombination detection)
namespace: operation
subset: operations
def: "Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment." [http://edamontology.org]
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid)


[Term]
id: EDAM_operation:0452
name: Sequence alignment analysis (indel detection)
namespace: operation
subset: operations
def: "Identify insertion, deletion and duplication events from a sequence alignment." [http://edamontology.org]
comment: Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid)


[Term]
id: EDAM_operation:0457
name: Nucleic acid stitch profile plotting
namespace: operation
subset: operations
def: "Calculate and plot a DNA or DNA/RNA stitch profile." [http://edamontology.org]
comment: A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.
is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting
relationship: has_output EDAM_data:1587 ! Nucleic acid stitch profile

[Term]
id: EDAM_operation:0458
name: Nucleic acid melting curve plotting
namespace: operation
subset: operations
def: "Calculate and plot a DNA or DNA/RNA melting curve." [http://edamontology.org]
is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting
relationship: has_output EDAM_data:2958 ! Nucleic acid melting curve

[Term]
id: EDAM_operation:0459
name: Nucleic acid probability profile plotting
namespace: operation
subset: operations
def: "Calculate and plot a DNA or DNA/RNA probability profile." [http://edamontology.org]
is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting
relationship: has_output EDAM_data:2959 ! Nucleic acid probability profile

[Term]
id: EDAM_operation:0460
name: Nucleic acid temperature profile plotting
namespace: operation
subset: operations
def: "Calculate and plot a DNA or DNA/RNA temperature profile." [http://edamontology.org]
is_a: EDAM_operation:0456 ! Nucleic acid melting profile plotting
relationship: has_output EDAM_data:2960 ! Nucleic acid temperature profile


[Term]
id: EDAM_operation:2444
name: Protein secondary structure processing
namespace: operation
subset: operations
def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org]
is_a: EDAM_operation:2482 ! Secondary structure processing
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_input EDAM_data:0876 {min_cardinality=0} ! Protein features (secondary structure)
relationship: has_output EDAM_data:0876 {min_cardinality=0} ! Protein features (secondary structure)
relationship: has_topic EDAM_topic:0694 ! Protein secondary structure

[Term]
id: EDAM_operation:0319
name: Protein secondary structure assignment
namespace: operation
subset: operations
def: "Assign secondary structure from protein coordinate or experimental data." [http://edamontology.org]
is_a: EDAM_operation:2444 ! Protein secondary structure processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_output EDAM_data:0876 {min_cardinality=1} ! Protein features (secondary structure)
relationship: has_topic EDAM_topic:2226 ! Structure determination

[Term]
id: EDAM_operation:0267
name: Protein secondary structure prediction
namespace: operation
subset: operations
def: "Predict secondary structure of protein sequences." [http://edamontology.org]
comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.
synonym: "Secondary structure prediction (protein)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2444 ! Protein secondary structure processing
is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence)
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_output EDAM_data:0876 {min_cardinality=1} ! Protein features (secondary structure)
relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction

[Term]
id: EDAM_operation:0268
name: Protein super-secondary structure prediction
namespace: operation
subset: operations
def: "Predict super-secondary structure of protein sequence(s)." [http://edamontology.org]
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
is_a: EDAM_operation:0267 ! Protein secondary structure prediction
relationship: has_output EDAM_data:0877 ! Protein features (super-secondary)

[Term]
id: EDAM_operation:0534
name: Protein secondary structure assignment (from coordinate data)
namespace: operation
subset: operations
def: "Assign secondary structure from protein coordinate data." [http://edamontology.org]
is_a: EDAM_operation:0319 ! Protein secondary structure assignment
is_a: EDAM_operation:3090 ! Protein feature prediction (from structure)

[Term]
id: EDAM_operation:0535
name: Protein secondary structure assignment (from CD data)
namespace: operation
subset: operations
def: "Assign secondary structure from circular dichroism (CD) spectroscopic data." [http://edamontology.org]
is_a: EDAM_operation:0319 ! Protein secondary structure assignment
relationship: has_input EDAM_data:0939 ! Protein circular dichroism (CD) spectroscopic data

[Term]
id: EDAM_operation:1847
name: DSSP secondary structure assignment
namespace: operation
subset: operations
def: "Determine for residue the DSSP determined secondary structure in three-state (HSC)." [http://edamontology.org, WHATIF]
xref: WHATIF: ResidueDSSP
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data)


[Term]
id: EDAM_operation:0467
name: Protein secondary structure prediction (integrated)
namespace: operation
subset: operations
def: "Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions." [http://edamontology.org]
is_a: EDAM_operation:0267 ! Protein secondary structure prediction

[Term]
id: EDAM_operation:0468
name: Protein secondary structure prediction (helices)
namespace: operation
subset: operations
def: "Predict helical secondary structure of protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0267 ! Protein secondary structure prediction


[Term]
id: EDAM_operation:0469
name: Protein secondary structure prediction (turns)
namespace: operation
subset: operations
def: "Predict turn structure (for example beta hairpin turns) of protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0267 ! Protein secondary structure prediction

[Term]
id: EDAM_operation:0470
name: Protein secondary structure prediction (coils)
namespace: operation
subset: operations
def: "Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0267 ! Protein secondary structure prediction

[Term]
id: EDAM_operation:0471
name: Protein secondary structure prediction (disulfide bonds)
namespace: operation
subset: operations
def: "Predict cysteine bonding state and disulfide bond partners in protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0267 ! Protein secondary structure prediction

[Term]
id: EDAM_operation:0269
name: Transmembrane protein prediction
namespace: operation
subset: operations
def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0270 ! Transmembrane protein analysis
is_a: EDAM_operation:0267 ! Protein secondary structure prediction
relationship: has_output EDAM_data:1456 {min_cardinality=1} ! Protein features (membrane regions)

[Term]
id: EDAM_operation:2456
name: GPCR classification
namespace: operation
subset: operations
def: "Classify G-protein coupled receptors (GPCRs) into families and subfamilies." [http://edamontology.org]
synonym: "G protein-coupled receptor (GPCR) classification" EXACT [http://edamontology.org]
is_a: EDAM_operation:0473 ! GPCR analysis
is_a: EDAM_operation:2995 ! Sequence classification
relationship: has_output EDAM_data:0907 {min_cardinality=1} ! Protein family


[Term]
id: EDAM_operation:2457
name: GPCR coupling selectivity prediction
namespace: operation
subset: operations
def: "Predict G-protein coupled receptor (GPCR) coupling selectivity." [http://edamontology.org]
is_a: EDAM_operation:0473 ! GPCR analysis
is_a: EDAM_operation:2492 ! Protein interaction prediction
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:0896 {min_cardinality=1} ! Protein report


[Term]
id: EDAM_operation:0473
name: GPCR analysis
namespace: operation
subset: operations
def: "Analyse G-protein coupled receptor proteins (GPCRs)." [http://edamontology.org]
synonym: "G protein-coupled receptor (GPCR) analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:0270 ! Transmembrane protein analysis
relationship: has_output EDAM_data:1456 ! Protein features (membrane regions)
relationship: has_topic EDAM_topic:0820 ! Membrane proteins


[Term]
id: EDAM_operation:0472
name: GPCR prediction
namespace: operation
subset: operations
def: "Predict G protein-coupled receptors (GPCR)." [http://edamontology.org]
synonym: "G protein-coupled receptor (GPCR) prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0269 ! Transmembrane protein prediction
is_a: EDAM_operation:0473 ! GPCR analysis

[Term]
id: EDAM_operation:0474
name: Protein structure prediction
namespace: operation
subset: operations
def: "Predict tertiary structure (backbone and side-chain conformation) of protein sequences." [http://edamontology.org]
is_a: EDAM_operation:0271 ! Structure prediction
is_a: EDAM_operation:2459 ! Structure processing (protein)
is_a: EDAM_operation:2479 ! Protein sequence analysis
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_output EDAM_data:1460 {min_cardinality=1} ! Protein structure
relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction

[Term]
id: EDAM_operation:0475
name: Nucleic acid structure prediction
namespace: operation
subset: operations
def: "Predict tertiary structure of DNA or RNA." [http://edamontology.org]
comment: Methods might identify thermodynamically stable or evolutionarily conserved structures.
is_a: EDAM_operation:0271 ! Structure prediction
is_a: EDAM_operation:2519 ! Structure processing (nucleic acid)
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:1459 {min_cardinality=1} ! Nucleic acid structure
relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction

[Term]
id: EDAM_operation:0476
name: Ab initio structure prediction
namespace: operation
subset: operations
def: "Predict tertiary structure of protein sequence(s) without homologs of known structure." [http://edamontology.org]
is_a: EDAM_operation:0474 ! Protein structure prediction
relationship: has_topic EDAM_topic:0174 ! Ab initio structure prediction


[Term]
id: EDAM_operation:0477
name: Protein modelling
namespace: operation
subset: operations
def: "Build a three-dimensional protein model based on known (for example homologs) structures." [http://edamontology.org]
comment: The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.
synonym: "Comparative modelling" EXACT [http://edamontology.org]
synonym: "Homology modelling" EXACT [http://edamontology.org]
synonym: "Homology structure modelling" EXACT [http://edamontology.org]
synonym: "Protein structure comparative modelling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2406 ! Protein structure analysis
is_a: EDAM_operation:0474 ! Protein structure prediction
is_a: EDAM_operation:2426 ! Modelling and simulation
relationship: has_topic EDAM_topic:0175 ! Homology modelling


[Term]
id: EDAM_operation:0478
name: Protein docking
namespace: operation
subset: operations
def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [http://edamontology.org]
comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.
is_a: EDAM_operation:0477 ! Protein modelling
is_a: EDAM_operation:2492 ! Protein interaction prediction
relationship: has_output EDAM_data:1461 {min_cardinality=0} ! Protein-ligand complex
relationship: has_output EDAM_data:2877 {min_cardinality=0} ! Protein complex
relationship: has_topic EDAM_topic:0177 ! Molecular docking


[Term]
id: EDAM_operation:0302
name: Protein threading
namespace: operation
subset: operations
def: "Align molecular sequence to structure in 3D space (threading)." [http://edamontology.org]
comment: Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
synonym: "Sequence-structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0303 ! Protein fold recognition
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:1460 {min_cardinality=1} ! Protein structure
relationship: has_output EDAM_data:0893 {min_cardinality=1} ! Sequence-structure alignment
relationship: has_topic EDAM_topic:0175 ! Homology modelling
relationship: has_topic EDAM_topic:0184 ! Threading


[Term]
id: EDAM_operation:0479
name: Protein modelling (backbone)
namespace: operation
subset: operations
def: "Model protein backbone conformation." [http://edamontology.org]
comment: Methods might require a preliminary C(alpha) trace.
is_a: EDAM_operation:0477 ! Protein modelling

[Term]
id: EDAM_operation:0480
name: Protein modelling (side chains)
namespace: operation
subset: operations
def: "Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc." [http://edamontology.org]
comment: Methods might use a residue rotamer library.
is_a: EDAM_operation:0477 ! Protein modelling

[Term]
id: EDAM_operation:0481
name: Protein modelling (loops)
namespace: operation
subset: operations
def: "Model loop conformation in protein structures." [http://edamontology.org]
is_a: EDAM_operation:0477 ! Protein modelling

[Term]
id: EDAM_operation:1841
name: Rotamer likelihood prediction
namespace: operation
subset: operations
def: "Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure." [http://edamontology.org, WHATIF]
comment: Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
xref: WHATIF:ShowLikelyRotamers
xref: WHATIF:ShowLikelyRotamers100
xref: WHATIF:ShowLikelyRotamers200
xref: WHATIF:ShowLikelyRotamers300
xref: WHATIF:ShowLikelyRotamers400
xref: WHATIF:ShowLikelyRotamers500
xref: WHATIF:ShowLikelyRotamers600
xref: WHATIF:ShowLikelyRotamers700
xref: WHATIF:ShowLikelyRotamers800
xref: WHATIF:ShowLikelyRotamers900
is_a: EDAM_operation:0480 ! Protein modelling (side chains)


[Term]
id: EDAM_operation:0482
name: Protein-ligand docking
namespace: operation
subset: operations
def: "Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques." [http://edamontology.org]
comment: Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.
synonym: "Virtual ligand screening" EXACT [http://edamontology.org]
is_a: EDAM_operation:0478 ! Protein docking
relationship: has_output EDAM_data:1461 {min_cardinality=1} ! Protein-ligand complex
relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions

[Term]
id: EDAM_operation:0483
name: Structured RNA prediction and optimisation
namespace: operation
subset: operations
def: "Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection." [http://edamontology.org]
synonym: "RNA inverse folding" EXACT [http://edamontology.org]
synonym: "Nucleic acid folding family identification" EXACT [http://edamontology.org]
is_a: EDAM_operation:3095 ! Nucleic acid design
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_output EDAM_data:1234 ! Sequence set (nucleic acid)
relationship: has_topic EDAM_topic:2953 ! Nucleic acid design

[Term]
id: EDAM_operation:0273
name: Protein interaction raw data analysis
namespace: operation
subset: operations
def: "Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org]
is_a: EDAM_operation:2949 ! Protein interaction analysis
relationship: has_input EDAM_data:0905 ! Protein interaction raw data
relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions

[Term]
id: EDAM_operation:2492
name: Protein interaction prediction
namespace: operation
subset: operations
def: "Predict the interactions of proteins with other molecules." [http://edamontology.org]
is_a: EDAM_operation:2405 ! Protein interaction data processing
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
relationship: has_output EDAM_data:0906 {min_cardinality=1} ! Protein interaction

[Term]
id: EDAM_operation:2464
name: Protein-protein interaction prediction
namespace: operation
subset: operations
def: "Identify or predict protein-protein interactions, interfaces, binding sites etc." [http://edamontology.org]
is_a: EDAM_operation:2492 ! Protein interaction prediction
relationship: has_output EDAM_data:1565 {min_cardinality=1} ! Protein-protein interaction
relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions


[Term]
id: EDAM_operation:0274
name: Protein-protein interaction prediction (from protein sequence)
namespace: operation
subset: operations
def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences." [http://edamontology.org]
is_a: EDAM_operation:2464 ! Protein-protein interaction prediction
is_a: EDAM_operation:3084 ! Protein function prediction (from sequence)

[Term]
id: EDAM_operation:0275
name: Protein-protein interaction prediction (from protein structure)
namespace: operation
subset: operations
def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org]
is_a: EDAM_operation:2464 ! Protein-protein interaction prediction
is_a: EDAM_operation:3090 ! Protein feature prediction (from structure)



[Term]
id: EDAM_operation:2445
name: Protein interaction network processing
namespace: operation
subset: operations
def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org]
is_a: EDAM_operation:2405 ! Protein interaction data processing
is_a: EDAM_operation:2438 ! Pathway or network processing
relationship: has_input EDAM_data:1663 {min_cardinality=0} ! Pathway or network (protein-protein interaction)
relationship: has_output EDAM_data:1663 {min_cardinality=0} ! Pathway or network (protein-protein interaction)
relationship: has_topic EDAM_topic:3044 ! Protein interaction networks

[Term]
id: EDAM_operation:0333
name: Zinc finger protein domain prediction and optimisation
namespace: operation
subset: operations
def: "Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases)." [http://edamontology.org]
is_a: EDAM_operation:0420 ! Protein-nucleic acid binding prediction
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_output EDAM_data:1567 ! Protein-nucleic acid interaction
relationship: has_topic EDAM_topic:0150 ! Protein design


[Term]
id: EDAM_operation:0276
name: Protein interaction network analysis
namespace: operation
subset: operations
def: "Analyse a network of protein interactions." [http://edamontology.org]
is_a: EDAM_operation:2445 ! Protein interaction network processing
is_a: EDAM_operation:2949 ! Protein interaction analysis
is_a: EDAM_operation:2497 ! Pathway or network analysis
relationship: has_input EDAM_data:1663 {min_cardinality=1} ! Pathway or network (protein-protein interaction)
relationship: has_output EDAM_data:2984 ! Pathway or network report

[Term]
id: EDAM_operation:0277
name: Protein interaction network comparison
namespace: operation
subset: operations
def: "Compare two or more networks of protein interactions." [http://edamontology.org]
is_a: EDAM_operation:0276 ! Protein interaction network analysis
is_a: EDAM_operation:1778 ! Protein function comparison
relationship: has_input EDAM_data:1663 {min_cardinality=2} ! Pathway or network (protein-protein interaction)



[Term]
id: EDAM_operation:3197 {since=1.1}
name: Genetic variation analysis
namespace: operation
subset: operations
def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org]
comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
synonym: "Sequence variation analysis" EXACT [http://edamontology.org]
synonym: "Genetic variation annotation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation)


[Term]
id: EDAM_operation:3227 {since=1.1}
name: Variant mapping
namespace: operation
subset: operations
def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org]
comment: Methods often utilise a database of aligned reads.
synonym: "Variant calling" EXACT [http://edamontology.org]
is_a: EDAM_operation:3197 ! Genetic variation analysis


[Term]
id: EDAM_operation:3228 {since=1.1}
name: Structural variation discovery
namespace: operation
subset: operations
def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org]
comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
is_a: EDAM_operation:3197 ! Genetic variation analysis


[Term]
id: EDAM_operation:3196 {since=1.1}
name: Genotyping
namespace: operation
subset: operations
def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org]
comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.
is_a: EDAM_operation:3197 ! Genetic variation analysis


! Link frameshift error detection and SNP detection to this one
[Term]
id: EDAM_operation:3202 {since=1.1}
name: Mutation detection
namespace: operation
subset: operations
def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org]
synonym: "Polymorphism detection" EXACT [http://edamontology.org]
is_a: EDAM_operation:3197 ! Genetic variation analysis


[Term]
id: EDAM_operation:0484
name: SNP detection
namespace: operation
subset: operations
def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org]
comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
synonym: "Single nucleotide polymorphism detection" EXACT [http://edamontology.org]
is_a: EDAM_operation:3202 ! Mutation detection
is_a: EDAM_operation:0415 ! Nucleic acid feature prediction
relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)


[Term]
id: EDAM_operation:3201 {since=1.1}
name: SNP calling
namespace: operation
subset: operations
def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org]
comment: Operations usually score confidence in the prediction or some other statistical measure of evidence.
is_a: EDAM_operation:0484 ! SNP detection


[Term]
id: EDAM_operation:0485
name: Radiation Hybrid Mapping
namespace: operation
subset: operations
def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers." [http://edamontology.org]
is_a: EDAM_operation:2944 ! Physical mapping
relationship: has_output EDAM_data:2870 {min_cardinality=1} ! Radiation hybrid map


[Term]
id: EDAM_operation:3186 {since=1.1}
name: Bisulfite mapping
namespace: operation
subset: operations
def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org]
comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.
synonym: "Bisulfite sequence mapping" EXACT [http://edamontology.org]
synonym: "Bisulfite sequence alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2944 ! Physical mapping


[Term]
id: EDAM_operation:0486
name: Functional mapping
namespace: operation
subset: operations
def: "Map the genetic architecture of dynamic complex traits." [http://edamontology.org]
comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0282 ! Genetic mapping


[Term]
id: EDAM_operation:0487
name: Haplotype inference
namespace: operation
subset: operations
def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [http://edamontology.org]
comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
synonym: "Haplotype mapping" EXACT [http://edamontology.org]
synonym: "Haplotype reconstruction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0283 ! Linkage analysis
relationship: has_output EDAM_data:1863 {min_cardinality=1} ! Haplotype map

[Term]
id: EDAM_operation:0488
name: Linkage disequilibrium calculation
namespace: operation
subset: operations
def: "Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org]
comment: Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.
is_a: EDAM_operation:0283 ! Linkage analysis
relationship: has_output EDAM_data:1634 {min_cardinality=1} ! Gene annotation (linkage disequilibrium)


[Term]
id: EDAM_operation:0286
name: Codon usage analysis
namespace: operation
subset: operations
! alt_id: EDAM_operation:2494
def: "Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences." [http://edamontology.org]
synonym: "synon: Codon usage table analysis" EXACT [http://edamontology.org]
synonym: "synon: Codon usage data analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:2501 ! Nucleic acid data processing
relationship: has_input EDAM_data:2977 {min_cardinality=0} ! Nucleic acid sequence
relationship: has_input EDAM_data:1597 {min_cardinality=0} ! Codon usage table
relationship: has_output EDAM_data:1597 {min_cardinality=0} ! Codon usage table
relationship: has_output EDAM_data:0914 {min_cardinality=0} ! Codon usage report
relationship: has_topic EDAM_topic:0107 ! Codon usage analysis


[Term]
id: EDAM_operation:2433
name: Codon usage table processing
namespace: operation
subset: operations
def: "Process (read and / or write) a codon usage table." [http://edamontology.org]
is_a: EDAM_operation:0286 ! Codon usage analysis
relationship: has_input EDAM_data:1597 {min_cardinality=0} ! Codon usage table
relationship: has_output EDAM_data:1597 {min_cardinality=0} ! Codon usage table

[Term]
id: EDAM_operation:0287
name: Base position variability plotting
namespace: operation
subset: operations
def: "Identify and plot third base position variability in a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_operation:0286 ! Codon usage analysis
relationship: has_output EDAM_data:1263 {min_cardinality=1} ! Sequence composition (base position variability)
relationship: has_topic EDAM_topic:0109 ! Gene finding


[Term]
id: EDAM_operation:0489
name: Genetic code prediction
namespace: operation
subset: operations
def: "Predict genetic code from analysis of codon usage data." [http://edamontology.org]
is_a: EDAM_operation:0286 ! Codon usage analysis
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:1598 {min_cardinality=1} ! Genetic code

[Term]
id: EDAM_operation:2962
name: Codon usage bias calculation
namespace: operation
subset: operations
def: "Calculate codon usage bias." [http://edamontology.org]
is_a: EDAM_operation:0286 ! Codon usage analysis
relationship: has_output EDAM_data:2865 {min_cardinality=1} ! Codon usage bias

[Term]
id: EDAM_operation:2963
name: Codon usage bias plotting
namespace: operation
subset: operations
def: "Generate a codon usage bias plot." [http://edamontology.org]
is_a: EDAM_operation:2962 ! Codon usage bias calculation
relationship: has_output EDAM_data:1600 {min_cardinality=1} ! Codon usage bias plot

[Term]
id: EDAM_operation:2964
name: Codon usage fraction calculation
namespace: operation
subset: operations
def: "Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc." [http://edamontology.org]
is_a: EDAM_operation:0286 ! Codon usage analysis
relationship: has_output EDAM_data:1602 {min_cardinality=1} ! Codon usage fraction difference



[Term]
id: EDAM_operation:0284
name: Codon usage table generation
namespace: operation
subset: operations
def: "Calculate codon usage statistics and create a codon usage table." [http://edamontology.org]
is_a: EDAM_operation:2433 ! Codon usage table processing
relationship: has_output EDAM_data:1597 {min_cardinality=1} ! Codon usage table

[Term]
id: EDAM_operation:0285
name: Codon usage table comparison
namespace: operation
subset: operations
def: "Compare two or more codon usage tables." [http://edamontology.org]
is_a: EDAM_operation:2433 ! Codon usage table processing
is_a: EDAM_operation:2998 ! Nucleic acid comparison


[Term]
id: EDAM_operation:3194 {since=1.1}
name: Genome feature comparison
namespace: operation
subset: operations
def: "Compare the features of two genome sequences." [http://edamontology.org]
comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.
is_a: EDAM_operation:0256 ! Feature comparison


[Term]
id: EDAM_operation:3182 {since=1.1}
name: Genome alignment construction
namespace: operation
subset: operations
def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org]
synonym: "Genome alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0292 ! Sequence alignment construction


[Term]
id: EDAM_operation:3198 {since=1.1}
name: Oligonucleotide alignment construction
namespace: operation
subset: operations
def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org]
comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.
synonym: "Short sequence read mapping" EXACT [http://edamontology.org]
synonym: "Short read mapping" EXACT [http://edamontology.org]
synonym: "Read mapping" EXACT [http://edamontology.org]
synonym: "Short oligonucleotide alignment" EXACT [http://edamontology.org]
synonym: "Oligonucleotide mapping" EXACT [http://edamontology.org]
synonym: "Oligonucleotide alignment" EXACT [http://edamontology.org]
synonym: "Short read alignment" EXACT [http://edamontology.org]
synonym: "Read alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0292 ! Sequence alignment construction


[Term]
id: EDAM_operation:3199 {since=1.1}
name: Split read mapping
namespace: operation
subset: operations
def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org]
is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction



[Term]
id: EDAM_operation:0491
name: Pairwise sequence alignment construction
namespace: operation
subset: operations
def: "Align exactly two molecular sequences." [http://edamontology.org]
synonym: "Pairwise sequence alignment" EXACT [http://edamontology.org]
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
is_a: EDAM_operation:0292 ! Sequence alignment construction
relationship: has_output EDAM_data:1381 {min_cardinality=1} ! Sequence alignment (pair)

[Term]
id: EDAM_operation:0492
name: Multiple sequence alignment construction
namespace: operation
subset: operations
def: "Align two or more molecular sequences." [http://edamontology.org]
synonym: "Multiple sequence alignment" EXACT [http://edamontology.org]
comment: This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.
is_a: EDAM_operation:0292 ! Sequence alignment construction

[Term]
id: EDAM_operation:2089
name: Sequence alignment refinement
namespace: operation
subset: operations
def: "Refine an existing sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2425 ! Optimisation and refinement


[Term]
id: EDAM_operation:0493
name: Pairwise sequence alignment construction (local)
namespace: operation
subset: operations
def: "Locally align exactly two molecular sequences." [http://edamontology.org]
synonym: "Pairwise sequence alignment (local)" EXACT [http://edamontology.org]
comment: Local alignment methods identify regions of local similarity.
synonym: "Local pairwise sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction

[Term]
id: EDAM_operation:0494
name: Pairwise sequence alignment construction (global)
namespace: operation
subset: operations
def: "Globally align exactly two molecular sequences." [http://edamontology.org]
synonym: "Pairwise sequence alignment (global)" EXACT [http://edamontology.org]
comment: Global alignment methods identify similarity across the entire length of the sequences.
synonym: "Global pairwise sequence alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0491 ! Pairwise sequence alignment construction

[Term]
id: EDAM_operation:0495
name: Multiple sequence alignment construction (local)
namespace: operation
subset: operations
def: "Locally align two or more molecular sequences." [http://edamontology.org]
synonym: "Multiple sequence alignment (local)" EXACT [http://edamontology.org]
comment: Local alignment methods identify regions of local similarity.
synonym: "Local multiple sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction

[Term]
id: EDAM_operation:0496
name: Multiple sequence alignment construction (global)
namespace: operation
subset: operations
def: "Globally align two or more molecular sequences." [http://edamontology.org]
synonym: "Multiple sequence alignment (global)" EXACT [http://edamontology.org]
comment: Global alignment methods identify similarity across the entire length of the sequences.
synonym: "Global multiple sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction

[Term]
id: EDAM_operation:0497
name: Multiple sequence alignment construction (constrained)
namespace: operation
subset: operations
def: "Align two or more molecular sequences with user-defined constraints." [http://edamontology.org]
synonym: "Multiple sequence alignment (constrained)" EXACT [http://edamontology.org]
synonym: "Constrained multiple sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction

[Term]
id: EDAM_operation:0498
name: Multiple sequence alignment construction (consensus)
namespace: operation
subset: operations
def: "Align two or more molecular sequences using multiple methods to achieve higher quality." [http://edamontology.org]
synonym: "Multiple sequence alignment (consensus)" EXACT [http://edamontology.org]
synonym: "Consensus multiple sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction

[Term]
id: EDAM_operation:0499
name: Multiple sequence alignment construction (phylogenetic tree-based)
namespace: operation
subset: operations
def: "Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree." [http://edamontology.org]
synonym: "Multiple sequence alignment (phylogenetic tree-based)" EXACT [http://edamontology.org]
comment: This is supposed to give a more biologically meaningful alignment than standard alignments.
synonym: "Phylogenetic tree-based multiple sequence alignment construction" EXACT [http.//edamontology.org]
is_a: EDAM_operation:0492 ! Multiple sequence alignment construction
relationship: has_topic EDAM_topic:0084 ! Phylogenetics


[Term]
id: EDAM_operation:0500
name: Secondary structure alignment construction
namespace: operation
subset: operations
def: "Align molecular secondary structure (represented as a 1D string)." [http://edamontology.org]
synonym: "Secondary structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2482 ! Secondary structure processing
is_a: EDAM_operation:2931 ! Secondary structure comparison
is_a: EDAM_operation:0294 ! Structure-based sequence alignment construction
relationship: has_output EDAM_data:2366 {min_cardinality=1} ! Secondary structure alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment


[Term]
id: EDAM_operation:0501
name: Protein secondary structure alignment construction
namespace: operation
subset: operations
def: "Align protein secondary structures." [http://edamontology.org]
synonym: "Protein secondary structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0500 ! Secondary structure alignment construction
is_a: EDAM_operation:2488 ! Protein secondary structure comparison
synonym: "Secondary structure alignment (protein)" EXACT [http://edamontology.org]
relationship: has_output EDAM_data:0878 {min_cardinality=1} ! Secondary structure alignment (protein)

[Term]
id: EDAM_operation:0502
name: RNA secondary structure alignment construction
namespace: operation
subset: operations
def: "Align RNA secondary structures." [http://edamontology.org]
synonym: "RNA secondary structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2439 ! RNA secondary structure processing
is_a: EDAM_operation:0500 ! Secondary structure alignment construction
synonym: "Secondary structure alignment (RNA)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:0880 {min_cardinality=2} ! RNA secondary structure record
relationship: has_output EDAM_data:0881 {min_cardinality=1} ! Secondary structure alignment (RNA)

[Term]
id: EDAM_operation:0503
name: Pairwise structure alignment construction
namespace: operation
subset: operations
def: "Align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org]
synonym: "Pairwise structure alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:0295 ! Structure alignment construction

[Term]
id: EDAM_operation:0504
name: Multiple structure alignment construction
namespace: operation
subset: operations
def: "Align (superimpose) two or more molecular tertiary structures." [http://edamontology.org]
synonym: "Multiple structure alignment" EXACT [http://edamontology.org]
comment: This includes methods that use an existing alignment.
is_a: EDAM_operation:0295 ! Structure alignment construction

[Term]
id: EDAM_operation:2488
name: Protein secondary structure comparison
namespace: operation
subset: operations
def: "Compare protein secondary structures." [http://edamontology.org]
synonym: "Protein secondary structure" EXACT [http://edamontology.org]
is_a: EDAM_operation:2416 ! Protein secondary structure analysis
is_a: EDAM_operation:2931 ! Secondary structure comparison
is_a: EDAM_operation:2997 ! Protein comparison
synonym: "Secondary structure comparison (protein)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:0876 {min_cardinality=2} ! Protein features (secondary structure)

[Term]
id: EDAM_operation:2487
name: Protein structure comparison
namespace: operation
subset: operations
def: "Compare protein tertiary structures." [http://edamontology.org]
comment: Methods might identify structural neighbors, find structural similarities or define a structural core.
is_a: EDAM_operation:2459 ! Structure processing (protein)
is_a: EDAM_operation:2483 ! Structure comparison
is_a: EDAM_operation:2997 ! Protein comparison
synonym: "Structure comparison (protein)" EXACT [http://edamontology.org]
relationship: has_input EDAM_data:1460 {min_cardinality=2} ! Protein structure
relationship: has_output EDAM_data:0897 ! Protein property



[Term]
id: EDAM_operation:2518
name: Nucleic acid structure comparison
namespace: operation
subset: operations
def: "Compare nucleic acid tertiary structures." [http://edamontology.org]
synonym: "Structure comparison (nucleic acid)" EXACT [http://edamontology.org]
is_a: EDAM_operation:2483 ! Structure comparison
is_a: EDAM_operation:2481 ! Nucleic acid structure analysis
is_a: EDAM_operation:2998 ! Nucleic acid comparison

[Term]
id: EDAM_operation:0505
name: Structure alignment (protein)
namespace: operation
subset: operations
def: "Align protein tertiary structures." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0295 ! Structure alignment construction

[Term]
id: EDAM_operation:0506
name: Structure alignment (RNA)
namespace: operation
subset: operations
def: "Align RNA tertiary structures." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_operation:0295 ! Structure alignment construction

[Term]
id: EDAM_operation:0507
name: Pairwise structure alignment construction (local)
namespace: operation
subset: operations
def: "Locally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org]
synonym: "Pairwise structure alignment (local)" EXACT [http://edamontology.org]
comment: Local alignment methods identify regions of local similarity, common substructures etc.
synonym: "Local pairwise structure alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0503 ! Pairwise structure alignment construction

[Term]
id: EDAM_operation:0508
name: Pairwise structure alignment construction (global)
namespace: operation
subset: operations
def: "Globally align (superimpose) exactly two molecular tertiary structures." [http://edamontology.org]
synonym: "Pairwise structure alignment (global)" EXACT [http://edamontology.org]
comment: Global alignment methods identify similarity across the entire structures.
synonym: "Global pairwise structure alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0503 ! Pairwise structure alignment construction

[Term]
id: EDAM_operation:0509
name: Multiple structure alignment construction (local)
namespace: operation
subset: operations
def: "Locally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org]
synonym: "Multiple structure alignment (local)" EXACT [http://edamontology.org]
comment: Local alignment methods identify regions of local similarity, common substructures etc.
synonym: "Local multiple structure alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0504 ! Multiple structure alignment construction

[Term]
id: EDAM_operation:0510
name: Multiple structure alignment construction (global)
namespace: operation
subset: operations
def: "Globally align (superimpose) two or more molecular tertiary structures." [http://edamontology.org]
synonym: "Multiple structure alignment (global)" EXACT [http://edamontology.org]
comment: Global alignment methods identify similarity across the entire structures.
synonym: "Global multiple structure alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0504 ! Multiple structure alignment construction

[Term]
id: EDAM_operation:0296
name: Sequence profile generation
namespace: operation
subset: operations
def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:2413 ! Sequence profile processing
is_a: EDAM_operation:2463 ! Sequence alignment processing
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
relationship: has_output EDAM_data:1354 {min_cardinality=1} ! Sequence profile

[Term]
id: EDAM_operation:0298
name: Sequence profile alignment construction
namespace: operation
subset: operations
def: "Align sequence profiles (representing sequence alignments)." [http://edamontology.org]
synonym: "Sequence profile alignment" EXACT [http://edamontology.org]
comment: See also 'Sequence alignment comparison'.
is_a: EDAM_operation:2413 ! Sequence profile processing
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:1354 {min_cardinality=2} ! Sequence profile
relationship: has_output EDAM_data:0868 {min_cardinality=1} ! Sequence profile alignment


[Term]
id: EDAM_operation:0300
name: Sequence-profile alignment construction
namespace: operation
subset: operations
def: "Align molecular sequence(s) to sequence profile(s)." [http://edamontology.org]
synonym: "Sequence-profile alignment" EXACT [http://edamontology.org]
comment: A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
is_a: EDAM_operation:2413 ! Sequence profile processing
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:1354 {min_cardinality=1} ! Sequence profile
relationship: has_output EDAM_data:0869 {min_cardinality=1} ! Sequence-profile alignment

[Term]
id: EDAM_operation:0511
name: Sequence profile alignment construction (pairwise)
namespace: operation
subset: operations
def: "Align exactly two molecular profiles." [http://edamontology.org]
synonym: "Sequence profile alignment (pairwise)" EXACT [http://edamontology.org]
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
synonym: "Pairwise sequence profile alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0298 ! Sequence profile alignment construction


[Term]
id: EDAM_operation:0512
name: Sequence profile alignment construction (multiple)
namespace: operation
subset: operations
def: "Align two or more molecular profiles." [http://edamontology.org]
synonym: "Sequence profile alignment (multiple)" EXACT [http://edamontology.org]
synonym: "Multiple sequence profile alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0298 ! Sequence profile alignment construction

[Term]
id: EDAM_operation:0297
name: Structural (3D) profile generation
namespace: operation
subset: operations
def: "Generate some type of structural (3D) profile or template from a structure or structure alignment." [http://edamontology.org]
synonym: "Structural profile generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2411 ! Structural (3D) profile processing
is_a: EDAM_operation:2952 ! Structure alignment processing
is_a: EDAM_operation:2465 ! Structure processing
relationship: has_input EDAM_data:0886  {min_cardinality=1} ! Structure alignment
relationship: has_input EDAM_data:0883 {min_cardinality=1} ! Structure
relationship: has_output EDAM_data:0889 {min_cardinality=1} ! Structural (3D) profile

[Term]
id: EDAM_operation:0299
name: Structural (3D) profile alignment construction
namespace: operation
subset: operations
def: "Align structural (3D) profiles or templates (representing structures or structure alignments)." [http://edamontology.org]
synonym: "Structural (3D) profile alignment" EXACT [http://edamontology.org]
synonym: "Structural profile alignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2411 ! Structural (3D) profile processing
is_a: EDAM_operation:2928 ! Alignment construction
relationship: has_input EDAM_data:0889 {min_cardinality=2} ! Structural (3D) profile
relationship: has_output EDAM_data:0890 {min_cardinality=1} ! Structural (3D) profile alignment
relationship: has_topic EDAM_topic:0183 ! Structure alignment

[Term]
id: EDAM_operation:0513
name: Structural (3D) profile alignment construction (pairwise)
namespace: operation
subset: operations
def: "Align exactly two molecular Structural (3D) profiles." [http://edamontology.org]
synonym: "Structural (3D) profile alignment (pairwise)" EXACT [http://edamontology.org]
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
synonym: "Pairwise structural (3D) profile alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction


[Term]
id: EDAM_operation:0514
name: Structural (3D) profile alignment construction (multiple)
namespace: operation
subset: operations
def: "Align two or more molecular 3D profiles." [http://edamontology.org]
synonym: "Structural (3D) profile alignment (multiple)" EXACT [http://edamontology.org]
synonym: "Multiple structural (3D) profile alignment construction" EXACT [http://edamontology.org]
is_a: EDAM_operation:0299 ! Structural (3D) profile alignment construction

[Term]
id: EDAM_operation:0301
name: Sequence-3D profile alignment construction
namespace: operation
subset: operations
def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [http://edamontology.org]
synonym: "Sequence-3D profile alignment" EXACT [http://edamontology.org]
comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
is_a: EDAM_operation:0303 ! Protein fold recognition
is_a: EDAM_operation:2928 ! Alignment construction
is_a: EDAM_operation:2403 ! Sequence analysis
relationship: has_input EDAM_data:0889 {min_cardinality=2} ! Structural (3D) profile
relationship: has_output EDAM_data:0891 {min_cardinality=1} ! Sequence-3D profile alignment
relationship: has_topic EDAM_topic:0184 ! Threading


[Term]
id: EDAM_operation:0308
name: PCR primer design
namespace: operation
subset: operations
def: "Design or predict oligonucleotide primers for PCR and DNA amplification etc." [http://edamontology.org]
comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
synonym: "PCR primer prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2419 ! Primer and probe design
relationship: has_input EDAM_data:2977 ! Nucleic acid sequence
relationship: has_output EDAM_data:1240 {min_cardinality=0} ! PCR primers
relationship: has_topic EDAM_topic:3032 ! Primer or probe design

[Term]
id: EDAM_operation:0309
name: Microarray probe design
namespace: operation
subset: operations
def: "Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families." [http://edamontology.org]
synonym: "Microarray probe prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2419 ! Primer and probe design
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_input EDAM_data:2977 ! Nucleic acid sequence
relationship: has_output EDAM_data:2717 {min_cardinality=1} ! Oligonucleotide probe annotation
relationship: has_topic EDAM_topic:0200 ! Microarrays
relationship: has_topic EDAM_topic:3032 ! Primer or probe design


[Term]
id: EDAM_operation:0307
name: Virtual PCR
namespace: operation
subset: operations
def: "Perform in-silico (virtual) PCR." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis


[Term]
id: EDAM_operation:3187
name: Sequence contamination filtering
namespace: operation
subset: operations
def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org]
is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis


[Term]
id: EDAM_operation:0517
name: PCR primer design (for large scale sequencing)
namespace: operation
subset: operations
def: "Predict primers for large scale sequencing." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design
relationship: has_topic EDAM_topic:3168 ! Sequencing

[Term]
id: EDAM_operation:0518
name: PCR primer design (for genotyping polymorphisms)
namespace: operation
subset: operations
def: "Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs)." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design

[Term]
id: EDAM_operation:0519
name: PCR primer design (for gene transcription profiling)
namespace: operation
subset: operations
def: "Predict primers for gene transcription profiling." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design
relationship: has_topic EDAM_topic:0203 ! Transcriptomics


[Term]
id: EDAM_operation:0520
name: PCR primer design (for conserved primers)
namespace: operation
subset: operations
def: "Predict primers that are conserved across multiple genomes or species." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design

[Term]
id: EDAM_operation:0521
name: PCR primer design (based on gene structure)
namespace: operation
subset: operations
def: "Predict primers based on gene structure, promoters, exon-exon junctions etc." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design
relationship: has_topic EDAM_topic:0109 ! Gene finding

[Term]
id: EDAM_operation:0522
name: PCR primer design (for methylation PCRs)
namespace: operation
subset: operations
def: "Predict primers for methylation PCRs." [http://edamontology.org]
is_a: EDAM_operation:0308 ! PCR primer design


[Term]
id: EDAM_operation:3183 {since=1.1}
name: Localized reassembly
namespace: operation
subset: operations
def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org]
is_a: EDAM_operation:0310 ! Sequence assembly


[Term]
id: EDAM_operation:0523
name: Sequence assembly (mapping assembly)
namespace: operation
subset: operations
def: "Sequence assembly by combining fragments using an existing backbone sequence." [http://edamontology.org]
comment: The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.
is_a: EDAM_operation:0310 ! Sequence assembly

[Term]
id: EDAM_operation:0524
name: Sequence assembly (de-novo assembly)
namespace: operation
subset: operations
def: "Sequence assembly by combining fragments into a new, previously unknown sequence." [http://edamontology.org]
comment: De-novo assemblers are much slower and more memory intensive than mapping assemblers.
is_a: EDAM_operation:0310 ! Sequence assembly

[Term]
id: EDAM_operation:0525
name: Sequence assembly (genome assembly)
namespace: operation
subset: operations
def: "Sequence assembly capable on a very large scale such as assembly of whole genomes." [http://edamontology.org]
is_a: EDAM_operation:0310 ! Sequence assembly

[Term]
id: EDAM_operation:0526
name: Sequence assembly (EST assembly)
namespace: operation
subset: operations
def: "Sequence assembly for EST sequences (transcribed mRNA)." [http://edamontology.org]
comment: Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.
is_a: EDAM_operation:0310 ! Sequence assembly

[Term]
id: EDAM_operation:2410
name: Gene expression analysis
namespace: operation
subset: operations
def: "Analyse gene expression and regulation data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:2435
name: Gene expression profile processing
namespace: operation
subset: operations
def: "Process (read and / or write) a gene expression profile." [http://edamontology.org]
is_a: EDAM_operation:2495 ! Gene expression data processing
relationship: has_input EDAM_data:0928 {min_cardinality=0} ! Gene expression profile
relationship: has_output EDAM_data:0928 {min_cardinality=0} ! Gene expression profile
relationship: has_topic EDAM_topic:0203 ! Transcriptomics



[Term]
id: EDAM_operation:0312
name: Sequencing-based expression profile data processing
namespace: operation
subset: operations
def: "Process (read and / or write) SAGE, MPSS or SBS experimental data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:2498
name: Sequencing-based expression profile data analysis
namespace: operation
subset: operations
def: "Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:2496
name: Gene regulatory network processing
namespace: operation
subset: operations
def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org]
is_a: EDAM_operation:2438 ! Pathway or network processing
relationship: has_input EDAM_data:2961 {min_cardinality=0} ! Pathway or network (gene regulation)
relationship: has_output EDAM_data:2961 {min_cardinality=0} ! Pathway or network (gene regulation)
relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks


[Term]
id: EDAM_operation:1781
name: Gene regulatory network analysis
namespace: operation
subset: operations
def: "Analyse a known network of gene regulation." [http://edamontology.org]
is_a: EDAM_operation:2496 ! Gene regulatory network processing
is_a: EDAM_operation:2497 ! Pathway or network analysis
relationship: has_input EDAM_data:2961 {min_cardinality=1} ! Pathway or network (gene regulation)


[Term]
id: EDAM_operation:2437
name: Gene regulatory network prediction
namespace: operation
subset: operations
def: "Predict a network of gene regulation." [http://edamontology.org]
is_a: EDAM_operation:2496 ! Gene regulatory network processing
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:2961 {min_cardinality=1} ! Pathway or network (gene regulation)


[Term]
id: EDAM_operation:3094 {since=beta13}
name: Protein interaction network prediction
namespace: operation
subset: operations
def: "Predict a network of protein interactions." [http://edamontology.org]
is_a: EDAM_operation:2445 ! Protein interaction network processing
relationship: has_output EDAM_data:1663 {min_cardinality=1} ! Pathway or network (protein-protein interaction)




[Term]
id: EDAM_operation:0316
name: Functional profiling
namespace: operation
subset: operations
def: "Interpret (in functional terms) and annotate gene expression data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0532 ! Gene expression profile analysis


[Term]
id: EDAM_operation:0264
name: Splice transcript prediction
namespace: operation
subset: operations
def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org]
is_a: EDAM_operation:2499 ! Splicing analysis
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_operation:2499
name: Splicing analysis
namespace: operation
subset: operations
def: "Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences." [http://edamontology.org]
synonym: "Splicing modelling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison
is_a: EDAM_operation:2426 ! Modelling and simulation
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_output EDAM_data:1307 {min_cardinality=1} ! Nucleic acid features (splice sites)
relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing

[Term]
id: EDAM_operation:0313
name: Gene expression profile clustering
namespace: operation
subset: operations
def: "Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles." [http://edamontology.org]
is_a: EDAM_operation:0315 ! Gene expression profile comparison
relationship: has_output EDAM_data:3111 ! Processed microarray data

[Term]
id: EDAM_operation:3223 {since=1.1}
name: Differential expression analysis
namespace: operation
subset: operations
def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org]
comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
synonym: "Differentially expressed gene identification" EXACT [http://edamontology.org]
is_a: EDAM_operation:0315 ! Gene expression profile comparison


[Term]
id: EDAM_operation:3224 {since=1.1}
name: Gene set testing
namespace: operation
subset: operations
def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org]
comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on.
is_a: EDAM_operation:2435 ! Gene expression profile processing


[Term]
id: EDAM_operation:0314
name: Gene expression profile generation
namespace: operation
subset: operations
def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org]
synonym: "Expression profiling" EXACT [http://edamontology.org]
synonym: "Gene expression profiling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2435 ! Gene expression profile processing
relationship: has_output EDAM_data:0928 {min_cardinality=1} ! Gene expression profile


[Term]
id: EDAM_operation:0315
name: Gene expression profile comparison
namespace: operation
subset: operations
def: "Compare gene expression profiles or patterns." [http://edamontology.org]
is_a: EDAM_operation:0532 ! Gene expression profile analysis
is_a: EDAM_operation:2998 ! Nucleic acid comparison
relationship: has_output EDAM_data:3111 ! Processed microarray data

[Term]
id: EDAM_operation:2436
name: Gene expression profile annotation
namespace: operation
subset: operations
def: "Annotate a gene expression profile with concepts from an ontology of gene functions." [http://edamontology.org]
is_a: EDAM_operation:0532 ! Gene expression profile analysis
is_a: EDAM_operation:0226 ! Annotation
relationship: has_output EDAM_data:0928 {min_cardinality=1} ! Gene expression profile

[Term]
id: EDAM_operation:0532
name: Gene expression profile analysis
namespace: operation
subset: operations
def: "Analyse one or more gene expression profiles, typically to interpret them in functional terms." [http://edamontology.org]
synonym: "Functional profiling" EXACT [http://edamontology.org]
is_a: EDAM_operation:2435 ! Gene expression profile processing
relationship: has_input EDAM_data:0928 {min_cardinality=1} ! Gene expression profile


[Term]
id: EDAM_operation:0533
name: Gene expression profile pathway mapping
namespace: operation
subset: operations
def: "Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway." [http://edamontology.org]
is_a: EDAM_operation:0532 ! Gene expression profile analysis
is_a: EDAM_operation:2497 ! Pathway or network analysis
relationship: has_output EDAM_data:2984 ! Pathway or network report


[Term]
id: EDAM_operation:3232 {since=1.1}
name: Gene expression QTL analysis
namespace: operation
subset: operations
def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org]
synonym: "eQTL profiling" EXACT [http://edamontology.org]
synonym: "expression QTL profiling" EXACT [http://edamontology.org]
synonym: "expression quantitative trait loci profiling" EXACT [http://edamontology.org]
is_a: EDAM_operation:0532 ! Gene expression profile analysis
relationship: has_output EDAM_data:2984 ! Pathway or network report


[Term]
id: EDAM_operation:0527
name: Tag mapping
namespace: operation
subset: operations
def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts." [http://edamontology.org]
comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.
synonym: "Tag to gene assignment" EXACT [http://edamontology.org]
is_a: EDAM_operation:2436 ! Gene expression profile annotation
relationship: has_output EDAM_data:0936 {min_cardinality=0} ! Sequence tag profile (with gene assignment)

[Term]
id: EDAM_operation:0528
name: SAGE data processing
namespace: operation
subset: operations
def: "Process (read and / or write) serial analysis of gene expression (SAGE) data." [http://edamontology.org]
synonym: "Serial analysis of gene expression data processing" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:0529
name: MPSS data processing
namespace: operation
subset: operations
def: "Process (read and / or write) massively parallel signature sequencing (MPSS) data." [http://edamontology.org]
synonym: "Massively parallel signature sequencing data processing" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:0530
name: SBS data processing
namespace: operation
subset: operations
def: "Process (read and / or write) sequencing by synthesis (SBS) data." [http://edamontology.org]
synonym: "Sequencing by synthesis data processing" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:2495 ! Gene expression data processing


[Term]
id: EDAM_operation:0531
name: Heat map generation
namespace: operation
subset: operations
def: "Generate a heat map of gene expression from microarray data." [http://edamontology.org]
comment: The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.
is_a: EDAM_operation:0571 ! Microarray data rendering
relationship: has_output EDAM_data:1636 {min_cardinality=1} ! Heat map


[Term]
id: EDAM_operation:2934
name: Microarray cluster textual view rendering
namespace: operation
subset: operations
def: "Visualise gene clusters with gene names." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2935
name: Microarray wave graph rendering
namespace: operation
subset: operations
synonym: "Microarray cluster temporal graph rendering" EXACT [http://edamontology.org]
def: "Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis." [http://edamontology.org]
comment: This view can be rendered as a pie graph.  The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2936
name: Microarray dendrograph rendering
namespace: operation
subset: operations
synonym: "Microarray checks view rendering" EXACT [http://edamontology.org]
synonym: "Microarray view rendering" EXACT [http://edamontology.org]
def: "Generate a dendrograph of raw, preprocessed or clustered microarray data." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2937
name: Microarray proximity map rendering
namespace: operation
subset: operations
synonym: "Microarray distance map rendering" EXACT [http://edamontology.org]
def: "Generate a plot of distances (distance matrix) between genes." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2938
name: Microarray tree or dendrogram view rendering
namespace: operation
subset: operations
synonym: "Microarray matrix tree plot rendering" EXACT [http://edamontology.org]
synonym: "Microarray 2-way dendrogram rendering" EXACT [http://edamontology.org]
def: "Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2939
name: Microarray principal component rendering
namespace: operation
subset: operations
def: "Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2940
name: Microarray scatter plot rendering
namespace: operation
subset: operations
def: "Generate a scatter plot of microarray data, typically after principal component analysis." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2941
name: Whole microarray graph view rendering
namespace: operation
subset: operations
def: "Visualise gene expression data where each band (or line graph) corresponds to a sample." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2942
name: Microarray tree-map rendering
namespace: operation
subset: operations
def: "Visualise gene expression data after hierarchical clustering for representing hierarchical relationships." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2943
name: Microarray Box-Whisker plot rendering
namespace: operation
subset: operations
def: "Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles." [http://edamontology.org]
is_a: EDAM_operation:0571 ! Microarray data rendering


[Term]
id: EDAM_operation:2459
name: Structure processing (protein)
namespace: operation
subset: operations
def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org]
is_a: EDAM_operation:2465 ! Structure processing
is_a: EDAM_operation:2502 ! Protein data processing
relationship: has_input EDAM_data:1460 {min_cardinality=0} ! Protein structure
relationship: has_output EDAM_data:1460 {min_cardinality=0} ! Protein structure
relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure


[Term]
id: EDAM_operation:0243
name: Protein property calculation (from structure)
namespace: operation
subset: operations
! alt_id: EDAM_operation:3089 {since=beta13} ! Not released
def: "Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure." [http://edamontology.org]
comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
is_a: EDAM_operation:2406 ! Protein structure analysis
is_a: EDAM_operation:0250 ! Protein property calculation
synonym: "Protein structural property calculation" EXACT [http://edamontology.org]
relationship: has_output EDAM_data:0897 {min_cardinality=0} ! Protein property
relationship: has_topic EDAM_topic:0123 ! Protein properties
relationship: has_topic EDAM_topic:2814 ! Protein structure analysis

[Term]
id: EDAM_operation:0244
name: Protein flexibility and motion analysis
namespace: operation
subset: operations
def: "Analyse flexibility and motion in protein structure." [http://edamontology.org]
comment: Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
is_a: EDAM_operation:2476 ! Molecular dynamics simulation
relationship: has_output EDAM_data:1541 {min_cardinality=1} ! Protein flexibility or motion report


[Term]
id: EDAM_operation:0245
name: Protein structural motif recognition
namespace: operation
subset: operations
def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org]
comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
synonym: "Protein structural feature identification" EXACT [http://edamontology.org]
is_a: EDAM_operation:3090 ! Protein feature prediction (from structure)
relationship: has_output EDAM_data:0899 {min_cardinality=1} ! Protein features (3D motif)
relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces

[Term]
id: EDAM_operation:0246
name: Protein domain recognition
namespace: operation
subset: operations
def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org]
is_a: EDAM_operation:3090 ! Protein feature prediction (from structure)
relationship: has_output EDAM_data:0901 {min_cardinality=1} ! Protein features (domains)
relationship: has_topic EDAM_topic:0736 ! Protein domains and folds


[Term]
id: EDAM_operation:0247
name: Protein architecture analysis
namespace: operation
subset: operations
def: "Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s)." [http://edamontology.org]
is_a: EDAM_operation:2406 ! Protein structure analysis
relationship: has_output EDAM_data:0902 {min_cardinality=1} ! Protein architecture report


[Term]
id: EDAM_operation:2474
name: Protein architecture comparison
namespace: operation
subset: operations
def: "Compare the architecture of two or more protein structures." [http://edamontology.org]
is_a: EDAM_operation:0247 ! Protein architecture analysis
is_a: EDAM_operation:2488 ! Protein secondary structure comparison
relationship: has_output EDAM_data:0902 {min_cardinality=1} ! Protein architecture report

[Term]
id: EDAM_operation:2475
name: Protein architecture recognition
namespace: operation
subset: operations
def: "Identify the architecture of a protein structure." [http://edamontology.org]
is_a: EDAM_operation:0247 ! Protein architecture analysis
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)
is_a: EDAM_operation:2996 ! Structure classification
relationship: has_output EDAM_data:0902 {min_cardinality=1} ! Protein architecture report

[Term]
id: EDAM_operation:0248
name: Residue interaction calculation
namespace: operation
subset: operations
def: "Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s)." [http://edamontology.org]
xref: WHATIF:ListContactsNormal
xref: WHATIF:ListContactsRelaxed
xref: WHATIF:ListSideChainContactsNormal
xref: WHATIF:ListSideChainContactsRelaxed
xref: WHATIF: SymShellOneXML
xref: WHATIF: SymShellTwoXML
xref: WHATIF: SymShellFiveXML
xref: WHATIF: SymShellTenXML
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
relationship: has_output EDAM_data:1540 {min_cardinality=1} ! Protein residue interactions
relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis


[Term]
id: EDAM_operation:0272
name: Residue interaction prediction
namespace: operation
subset: operations
def: "Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences." [http://edamontology.org]
comment: Methods usually involve multiple sequence alignment analysis.
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
is_a: EDAM_operation:2506 ! Sequence alignment analysis (protein)
relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis


[Term]
id: EDAM_operation:0249
name: Torsion angle calculation
namespace: operation
subset: operations
def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [http://edamontology.org]
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
relationship: has_output EDAM_data:2991 ! Protein torsion angle data

[Term]
id: EDAM_operation:0320
name: Protein structure assignment
namespace: operation
subset: operations
def: "Assign a protein tertiary structure (3D coordinates) from raw experimental data." [http://edamontology.org]
is_a: EDAM_operation:2459 ! Structure processing (protein)
relationship: has_output EDAM_data:1460 {min_cardinality=1} ! Protein structure
relationship: has_topic EDAM_topic:2226 ! Structure determination


[Term]
id: EDAM_operation:0321
name: Protein model evaluation
namespace: operation
subset: operations
def: "Evaluate the quality or correctness a protein three-dimensional model." [http://edamontology.org]
comment: Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.
xref: WHATIF: UseFileDB
is_a: EDAM_operation:0477 ! Protein modelling
is_a: EDAM_operation:2428 ! Evaluation and validation
relationship: has_output EDAM_data:1539 {min_cardinality=1} ! Protein structural quality report
relationship: has_topic EDAM_topic:2275 ! Molecular modelling
relationship: has_topic EDAM_topic:0175 ! Homology modelling
relationship: has_topic EDAM_topic:0179 ! Protein tertiary structure prediction

[Term]
id: EDAM_operation:0322
name: Protein model refinement
namespace: operation
subset: operations
def: "Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc." [http://edamontology.org]
comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
xref: WHATIF: CorrectedPDBasXML
is_a: EDAM_operation:0321 ! Protein model evaluation
is_a: EDAM_operation:2425 ! Optimisation and refinement


[Term]
id: EDAM_operation:2239
name: 3D-1D scoring matrix generation
namespace: operation
subset: operations
def: "Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data." [http://edamontology.org]
comment: A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1499 {min_cardinality=1} ! 3D-1D scoring matrix
relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles


[Term]
id: EDAM_operation:2574
name: Protein hydropathy calculation
namespace: operation
subset: operations
def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information)." [http://edamontology.org]
is_a: EDAM_operation:0250 ! Protein property calculation
relationship: has_output EDAM_data:2970 {min_cardinality=1} ! Protein hydropathy data
relationship: has_topic EDAM_topic:0137 ! Protein hydropathy


[Term]
id: EDAM_operation:0383
name: Protein hydropathy calculation (from structure)
namespace: operation
subset: operations
def: "Analyse the hydrophobic, hydrophilic or charge properties of a protein structure." [http://edamontology.org]
is_a: EDAM_operation:2574 ! Protein hydropathy calculation
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)


[Term]
id: EDAM_operation:0384
name: Protein solvent accessibility calculation
namespace: operation
subset: operations
def: "Calculate solvent accessible or buried surface areas in protein structures." [http://edamontology.org]
is_a: EDAM_operation:0243 ! Protein property calculation (from structure)
relationship: has_output EDAM_data:1542 ! Protein solvent accessibility
relationship: has_topic EDAM_topic:0137 ! Protein hydropathy

[Term]
id: EDAM_operation:1850
name: Protein cysteine and disulfide bond assignment
namespace: operation
subset: operations
def: "Assign cysteine bonding state and disulfide bond partners in protein structures." [http://edamontology.org]
is_a: EDAM_operation:0534 ! Protein secondary structure assignment (from coordinate data)
relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis

[Term]
id: EDAM_operation:0385
name: Protein hydropathy cluster calculation
namespace: operation
subset: operations
def: "Identify clusters of hydrophobic or charged residues in a protein structure." [http://edamontology.org]
is_a: EDAM_operation:0383 ! Protein hydropathy calculation (from structure)
is_a: EDAM_operation:0393 ! Protein residue cluster calculation

[Term]
id: EDAM_operation:0386
name: Protein dipole moment calculation
namespace: operation
subset: operations
def: "Calculate whether a protein structure has an unusually large net charge (dipole moment)." [http://edamontology.org]
is_a: EDAM_operation:3088 ! Protein property calculation (from sequence)
relationship: has_output EDAM_data:1545 {min_cardinality=1} ! Protein dipole moment

[Term]
id: EDAM_operation:0387
name: Protein surface and interior calculation
namespace: operation
subset: operations
def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [http://edamontology.org]
is_a: EDAM_operation:0384 ! Protein solvent accessibility calculation
relationship: has_output EDAM_data:1543 {min_cardinality=1} ! Protein surface report
relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces


[Term]
id: EDAM_operation:1816
name: Surface rendering
namespace: operation
subset: operations
def: "Calculate the positions of dots that are homogeneously distributed over the surface of a molecule." [http://edamontology.org, WHATIF]
comment: A dot has three coordinates (x,y,z) and (typically) a color.
xref: WHATIF:GetSurfaceDots
is_a: EDAM_operation:2462 ! Protein surface calculation
is_a: EDAM_operation:0570 ! Structure rendering



[Term]
id: EDAM_operation:2460
name: Protein atom surface calculation
namespace: operation
subset: operations
def: "Calculate the solvent accessibility for each atom in a structure." [http://edamontology.org, WHATIF]
comment: Waters are not considered.
is_a: EDAM_operation:0387 ! Protein surface and interior calculation


[Term]
id: EDAM_operation:1817
name: Protein atom surface calculation (accessible)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible surface') for each atom in a structure." [http://edamontology.org, WHATIF]
comment: Waters are not considered.
xref: WHATIF:AtomAccessibilitySolvent
xref: WHATIF:AtomAccessibilitySolventPlus
is_a: EDAM_operation:2460 ! Protein atom surface calculation


[Term]
id: EDAM_operation:1818
name: Protein atom surface calculation (accessible molecular)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure." [http://edamontology.org, WHATIF]
comment: Waters are not considered.
xref: WHATIF:AtomAccessibilityMolecular
xref: WHATIF:AtomAccessibilityMolecularPlus
is_a: EDAM_operation:2460 ! Protein atom surface calculation


[Term]
id: EDAM_operation:2461
name: Protein residue surface calculation
namespace: operation
subset: operations
def: "Calculate the solvent accessibility for each residue in a structure." [http://edamontology.org, WHATIF]
is_a: EDAM_operation:0387 ! Protein surface and interior calculation


[Term]
id: EDAM_operation:1819
name: Protein residue surface calculation (accessible)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible surface') for each residue in a structure." [http://edamontology.org, WHATIF]
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
xref: WHATIF:ResidueAccessibilitySolvent
is_a: EDAM_operation:2461 ! Protein residue surface calculation


[Term]
id: EDAM_operation:1820
name: Protein residue surface calculation (vacuum accessible)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF]
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
xref: WHATIF:ResidueAccessibilityVacuum
is_a: EDAM_operation:2461 ! Protein residue surface calculation


[Term]
id: EDAM_operation:1821
name: Protein residue surface calculation (accessible molecular)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure." [http://edamontology.org, WHATIF]
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
xref: WHATIF:ResidueAccessibilityMolecular
is_a: EDAM_operation:2461 ! Protein residue surface calculation

[Term]
id: EDAM_operation:1822
name: Protein residue surface calculation (vacuum molecular)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to." [http://edamontology.org, WHATIF]
comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
xref: WHATIF:ResidueAccessibilityVacuumMolecular
is_a: EDAM_operation:2461 ! Protein residue surface calculation


[Term]
id: EDAM_operation:2462
name: Protein surface calculation
namespace: operation
subset: operations
def: "Calculate the solvent accessibility of a structure as a whole." [http://edamontology.org, WHATIF]
is_a: EDAM_operation:0387 ! Protein surface and interior calculation


[Term]
id: EDAM_operation:1823
name: Protein surface calculation (accessible molecular)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole." [http://edamontology.org, WHATIF]
xref: WHATIF:TotAccessibilityMolecular
is_a: EDAM_operation:2462 ! Protein surface calculation


[Term]
id: EDAM_operation:1824
name: Protein surface calculation (accessible)
namespace: operation
subset: operations
def: "Calculate the solvent accessibility ('accessible surface') for a structure as a whole." [http://edamontology.org, WHATIF]
xref: WHATIF:TotAccessibilitySolvent
is_a: EDAM_operation:2462 ! Protein surface calculation

[Term]
id: EDAM_operation:1829
name: Cysteine bridge detection
namespace: operation
subset: operations
def: "Detect cysteine bridges (from coordinate data) in a protein structure." [http://edamontology.org, WHATIF]
xref: WHATIF:ShowCysteineBridge
is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment


[Term]
id: EDAM_operation:1830
name: Free cysteine detection
namespace: operation
subset: operations
def: "Detect free cysteines in a protein structure." [http://edamontology.org, WHATIF]
comment: A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.
xref: WHATIF:ShowCysteineFree
is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment


[Term]
id: EDAM_operation:1831
name: Metal-bound cysteine detection
namespace: operation
subset: operations
def: "Detect cysteines that are bound to metal in a protein structure." [http://edamontology.org, WHATIF]
xref: WHATIF:ShowCysteineMetal
is_a: EDAM_operation:1850 ! Protein cysteine and disulfide bond assignment

[Term]
id: EDAM_operation:2575
name: Binding site prediction
namespace: operation
subset: operations
def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org]
synonym: "Ligand-binding and active site prediction" EXACT [http://edamontology.org]
is_a: EDAM_operation:2492 ! Protein interaction prediction
relationship: has_output EDAM_data:1325 {min_cardinality=0} ! Protein features (active sites)
relationship: has_output EDAM_data:1326 {min_cardinality=0} ! Protein features (binding sites)
relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions

[Term]
id: EDAM_operation:0388
name: Binding site prediction (from structure)
namespace: operation
subset: operations
def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures." [http://edamontology.org]
synonym: "Ligand-binding and active site prediction (from structure)" EXACT [http://edamontology.org]
is_a: EDAM_operation:0245 ! Protein structural motif recognition
is_a: EDAM_operation:2575 ! Binding site prediction


[Term]
id: EDAM_operation:0389
name: Protein-nucleic acid binding site analysis
namespace: operation
subset: operations
def: "Analyse RNA or DNA-binding sites in protein structure." [http://edamontology.org]
is_a: EDAM_operation:2949 ! Protein interaction analysis
relationship: has_input EDAM_data:1567 ! Protein-nucleic acid interaction
relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions

[Term]
id: EDAM_operation:0390
name: Protein peeling
namespace: operation
subset: operations
def: "Decompose a structure into compact or globular fragments (protein peeling)." [http://edamontology.org]
is_a: EDAM_operation:0246 ! Protein domain recognition
relationship: has_output EDAM_data:0901 {min_cardinality=1} ! Protein features (domains)


[Term]
id: EDAM_operation:0391
name: Protein distance matrix calculation
namespace: operation
subset: operations
def: "Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org]
is_a: EDAM_operation:0248 ! Residue interaction calculation
relationship: has_output EDAM_data:1546 {min_cardinality=1} ! Protein distance matrix

[Term]
id: EDAM_operation:0394
name: Hydrogen bond calculation
namespace: operation
subset: operations
def: "Identify potential hydrogen bonds between amino acids and other groups." [http://edamontology.org, WHATIF]
comment: The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.
xref: WHATIF:ShowHydrogenBondsM
xref: WHATIF:ShowHydrogenBonds
xref: WHATIF:ShowHydrogenBonds
xref: WHATIF:HasHydrogenBonds
is_a: EDAM_operation:0248 ! Residue interaction calculation
relationship: has_output EDAM_data:1549 {min_cardinality=1} ! Protein hydrogen bonds


[Term]
id: EDAM_operation:2491
name: Hydrogen bond calculation (inter-residue)
namespace: operation
subset: operations
def: "Identify potential hydrogen bonds between amino acid residues." [http://edamontology.org, WHATIF]
is_a: EDAM_operation:0394 ! Hydrogen bond calculation
is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue)

[Term]
id: EDAM_operation:1839
name: Salt bridge calculation
namespace: operation
subset: operations
def: "Calculate (and possibly score) salt bridges in a protein structure." [http://edamontology.org, WHATIF]
comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
xref: WHATIF:HasSaltBridge
xref: WHATIF:HasSaltBridgePlus
xref: WHATIF:ShowSaltBridges
xref: WHATIF:ShowSaltBridgesH
is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue)

[Term]
id: EDAM_operation:1846
name: HET group detection
namespace: operation
subset: operations
def: "Identify HET groups in PDB files." [http://edamontology.org, WHATIF]
comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
xref: WHATIF: HETGroupNames
is_a: EDAM_operation:1838 ! Residue contact calculation (residue-ligand)


[Term]
id: EDAM_operation:2950
! alt_id: EDAM_operation:1833
name: Residue contact calculation
namespace: operation
subset: operations
def: "Calculate contacts between residues and some other group in a protein structure." [http://edamontology.org, WHATIF]
is_a: EDAM_operation:0248 ! Residue interaction calculation


[Term]
id: EDAM_operation:1838
name: Residue contact calculation (residue-ligand)
namespace: operation
subset: operations
def: "Calculate contacts between residues and ligands in a protein structure." [http://edamontology.org, WHATIF]
xref: WHATIF:ShowLigandContacts
xref: WHATIF:ShowDrugContacts
xref: WHATIF:ShowDrugContactsShort
is_a: EDAM_operation:2950 ! Residue contact calculation
is_a: EDAM_operation:0388 ! Binding site prediction (from structure)


[Term]
id: EDAM_operation:2490
name: Residue contact calculation (residue-residue)
namespace: operation
subset: operations
def: "Calculate contacts between residues in a protein structure." [http://edamontology.org, WHATIF]
is_a: EDAM_operation:2950 ! Residue contact calculation


[Term]
id: EDAM_operation:0392
name: Protein contact map calculation
namespace: operation
subset: operations
def: "Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure." [http://edamontology.org]
is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue)
relationship: has_output EDAM_data:1547 {min_cardinality=1} ! Protein contact map


[Term]
id: EDAM_operation:0393
name: Protein residue cluster calculation
namespace: operation
subset: operations
def: "Calculate clusters of contacting residues in protein structures." [http://edamontology.org]
comment: Cluster of contacting residues might be key structural residues.
is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue)
relationship: has_output EDAM_data:1548 {min_cardinality=1} ! Protein residue 3D cluster


[Term]
id: EDAM_operation:1832
name: Residue contact calculation (residue-nucleic acid)
namespace: operation
subset: operations
def: "Calculate protein residue contacts with nucleic acids in a structure." [http://edamontology.org, WHATIF]
xref: WHATIF:HasNucleicContacts
xref: WHATIF:ShowProteiNucleicContacts
is_a: EDAM_operation:2950 ! Residue contact calculation
is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis
is_a: EDAM_operation:0245 ! Protein structural motif recognition


[Term]
id: EDAM_operation:1834
name: Residue contact calculation (residue-metal)
namespace: operation
subset: operations
def: "Calculate protein residue contacts with metal in a structure." [http://edamontology.org, WHATIF]
xref: WHATIF:HasMetalContacts
xref: WHATIF:HasMetalContactsPlus
is_a: EDAM_operation:2950 ! Residue contact calculation
is_a: EDAM_operation:0388 ! Binding site prediction (from structure)


[Term]
id: EDAM_operation:1835
name: Residue contact calculation (residue-negative ion)
namespace: operation
subset: operations
def: "Calculate ion contacts in a structure (all ions for all side chain atoms)." [http://edamontology.org, WHATIF]
xref: WHATIF:HasNegativeIonContacts
xref: WHATIF:HasNegativeIonContactsPlus
is_a: EDAM_operation:2950 ! Residue contact calculation

[Term]
id: EDAM_operation:1837
name: Residue symmetry contact calculation
namespace: operation
subset: operations
def: "Calculate the number of symmetry contacts made by residues in a protein structure." [http://edamontology.org, WHATIF]
comment: A symmetry contact is a contact between two atoms in different asymmetric unit.
xref: WHATIF:SymmetryContact
is_a: EDAM_operation:2490 ! Residue contact calculation (residue-residue)

[Term]
id: EDAM_operation:0396
name: Ramachandran plot calculation
namespace: operation
subset: operations
def: "Calculate a Ramachandran plot of a protein structure." [http://edamontology.org]
is_a: EDAM_operation:0249 ! Torsion angle calculation
relationship: has_output EDAM_data:1544 {min_cardinality=1} ! Ramachandran plot


[Term]
id: EDAM_operation:0397
name: Ramachandran plot evaluation
namespace: operation
subset: operations
def: "Analyse (typically to validate) a Ramachandran plot of a protein structure." [http://edamontology.org]
is_a: EDAM_operation:1844 ! Dihedral angle validation
relationship: has_input EDAM_data:1544 {min_cardinality=1} ! Ramachandran plot
relationship: has_output EDAM_data:1539 ! Protein structural quality report

[Term]
id: EDAM_operation:1825
name: Backbone torsion angle calculation
namespace: operation
subset: operations
def: "Calculate for each residue in a protein structure all its backbone torsion angles." [http://edamontology.org, WHATIF]
xref: WHATIF:ResidueTorsionsBB
is_a: EDAM_operation:0249 ! Torsion angle calculation


[Term]
id: EDAM_operation:1826
name: Full torsion angle calculation
namespace: operation
subset: operations
def: "Calculate for each residue in a protein structure all its torsion angles." [http://edamontology.org, WHATIF]
xref: WHATIF:ResidueTorsions
is_a: EDAM_operation:0249 ! Torsion angle calculation


[Term]
id: EDAM_operation:1827
name: Cysteine torsion angle calculation
namespace: operation
subset: operations
def: "Calculate for each cysteine (bridge) all its torsion angles." [http://edamontology.org, WHATIF]
xref: WHATIF:CysteineTorsions
is_a: EDAM_operation:0249 ! Torsion angle calculation


[Term]
id: EDAM_operation:1828
name: Tau angle calculation
namespace: operation
subset: operations
def: "For each amino acid in a protein structure calculate the backbone angle tau." [http://edamontology.org, WHATIF]
comment: Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
xref: WHATIF:ShowTauAngle
is_a: EDAM_operation:0249 ! Torsion angle calculation


[Term]
id: EDAM_operation:0536
name: Protein structure assignment (from X-ray crystallographic data)
namespace: operation
subset: operations
def: "Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data." [http://edamontology.org]
is_a: EDAM_operation:0320 ! Protein structure assignment
relationship: has_input EDAM_data:0937 {min_cardinality=1} ! Protein X-ray crystallographic data

[Term]
id: EDAM_operation:0537
name: Protein structure assignment (from NMR data)
namespace: operation
subset: operations
def: "Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data." [http://edamontology.org]
is_a: EDAM_operation:0320 ! Protein structure assignment
relationship: has_input EDAM_data:0938 {min_cardinality=1} ! Protein NMR data

[Term]
id: EDAM_operation:0395
name: Residue non-canonical interaction detection
namespace: operation
subset: operations
def: "Calculate non-canonical atomic interactions in protein structures." [http://edamontology.org]
is_a: EDAM_operation:0248 ! Residue interaction calculation
is_a: EDAM_operation:0321 ! Protein model evaluation
relationship: has_output EDAM_data:1550 {min_cardinality=1} ! Protein non-canonical interactions

[Term]
id: EDAM_operation:1913
name: Residue validation
namespace: operation
subset: operations
def: "Identify poor quality amino acid positions in protein structures." [http://edamontology.org, WHATIF]
comment: The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).
xref: WHATIF: UseResidueDB
is_a: EDAM_operation:0321 ! Protein model evaluation

[Term]
id: EDAM_operation:1843
name: Residue packing validation
namespace: operation
subset: operations
def: "Identify poorly packed residues in protein structures." [http://edamontology.org, WHATIF]
xref: WHATIF: PackingQuality
is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection

[Term]
id: EDAM_operation:1844
name: Dihedral angle validation
namespace: operation
subset: operations
def: "Identify for each residue in a protein structure any improper dihedral (phi/psi) angles." [http://edamontology.org, WHATIF]
xref: WHATIF: ImproperQualitySum
xref: WHATIF: ImproperQualityMax
is_a: EDAM_operation:0321 ! Protein model evaluation

[Term]
id: EDAM_operation:1836
name: Residue bump detection
namespace: operation
subset: operations
def: "Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance." [http://edamontology.org, WHATIF]
xref: WHATIF:ShowBumps
is_a: EDAM_operation:0395 ! Residue non-canonical interaction detection




[Term]
id: EDAM_operation:2443
name: Phylogenetic tree processing
namespace: operation
subset: operations
def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:0872 {min_cardinality=0} ! Phylogenetic tree
relationship: has_output EDAM_data:0872 {min_cardinality=0} ! Phylogenetic tree
relationship: has_topic EDAM_topic:0084 ! Phylogenetics


[Term]
id: EDAM_operation:0550
name: Sequence alignment analysis (phylogenetic modelling)
namespace: operation
subset: operations
def: "Identify a plausible model of DNA substitution that explains a DNA sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:2507 ! Sequence alignment analysis (nucleic acid)
is_a: EDAM_operation:2426 ! Modelling and simulation
relationship: has_output EDAM_data:1439 ! DNA substitution model
relationship: has_topic EDAM_topic:0084 ! Phylogenetics


[Term]
id: EDAM_operation:0554
name: Phylogenetic tree analysis (natural selection)
namespace: operation
subset: operations
def: "Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive)." [http://edamontology.org]
comment: Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.
is_a: EDAM_operation:0324 ! Phylogenetic tree analysis


[Term]
id: EDAM_operation:0323
name: Phylogenetic tree construction
namespace: operation
subset: operations
def: "Construct a phylogenetic tree." [http://edamontology.org]
synonym: "Phylogenetic tree construction" EXACT [http://edamontology.org]
comment: Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.
synonym: "Phylogenetic tree generation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2443 ! Phylogenetic tree processing
is_a: EDAM_operation:2995 ! Sequence classification
relationship: has_output EDAM_data:0872 {min_cardinality=1} ! Phylogenetic tree
relationship: has_topic EDAM_topic:0080 ! Sequence analysis
relationship: has_topic EDAM_topic:0084 ! Phylogenetics


[Term]
id: EDAM_operation:0325
name: Phylogenetic tree comparison
namespace: operation
subset: operations
def: "Compare two or more phylogenetic trees." [http://edamontology.org]
comment: For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.
is_a: EDAM_operation:0324 ! Phylogenetic tree analysis
is_a: EDAM_operation:2424 ! Comparison

[Term]
id: EDAM_operation:0326
name: Phylogenetic tree editing
namespace: operation
subset: operations
def: "Edit a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_operation:2443 ! Phylogenetic tree processing
is_a: EDAM_operation:3096 ! Editing
relationship: has_input EDAM_data:0872 {min_cardinality=1} ! Phylogenetic tree
relationship: has_output EDAM_data:0872 {min_cardinality=1} ! Phylogenetic tree


[Term]
id: EDAM_operation:0551
name: Phylogenetic tree analysis (shape)
namespace: operation
subset: operations
def: "Analyse the shape (topology) of a phylogenetic tree." [http://edamontology.org]
synonym: "Phylogenetic tree topology analysis" EXACT [http://edamontology.org]
is_a: EDAM_operation:0324 ! Phylogenetic tree analysis
relationship: has_output EDAM_data:1440 {min_cardinality=1} ! Phylogenetic tree report (tree shape)

[Term]
id: EDAM_operation:0552
name: Phylogenetic tree bootstrapping
namespace: operation
subset: operations
def: "Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_operation:0324 ! Phylogenetic tree analysis
is_a: EDAM_operation:2428 ! Evaluation and validation
relationship: has_output EDAM_data:1441 {min_cardinality=1} ! Phylogenetic tree report (tree evaluation)


[Term]
id: EDAM_operation:0553
name: Phylogenetic tree analysis (gene family prediction)
namespace: operation
subset: operations
def: "Predict families of genes and gene function based on their position in a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_operation:0324 ! Phylogenetic tree analysis
relationship: has_output EDAM_data:0916 ! Gene annotation
relationship: has_topic EDAM_topic:0194 ! Phylogenomics

[Term]
id: EDAM_operation:0538
name: Phylogenetic tree construction (data centric)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree from a specific type of data." [http://edamontology.org]
is_a: EDAM_operation:0323 ! Phylogenetic tree construction

[Term]
id: EDAM_operation:0539
name: Phylogenetic tree construction (method centric)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree using a specific method." [http://edamontology.org]
is_a: EDAM_operation:0323 ! Phylogenetic tree construction

[Term]
id: EDAM_operation:0540
name: Phylogenetic tree construction (from molecular sequences)
namespace: operation
subset: operations
def: "Phylogenetic tree construction from molecular sequences." [http://edamontology.org]
comment: Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.
is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric)
is_a: EDAM_operation:2403 ! Sequence analysis


[Term]
id: EDAM_operation:0541
name: Phylogenetic tree construction (from continuous quantitative characters)
namespace: operation
subset: operations
def: "Phylogenetic tree construction from continuous quantitative character data." [http://edamontology.org]
is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric)
relationship: has_input EDAM_data:1426 {min_cardinality=1} ! Phylogenetic continuous quantitative data


[Term]
id: EDAM_operation:0542
name: Phylogenetic tree construction (from gene frequencies)
namespace: operation
subset: operations
def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org]
is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric)
relationship: has_input EDAM_data:2873 {min_cardinality=1} ! Phylogenetic gene frequencies data
relationship: has_topic EDAM_topic:0203 ! Transcriptomics


[Term]
id: EDAM_operation:0543
name: Phylogenetic tree construction (from polymorphism data)
namespace: operation
subset: operations
def: "Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data." [http://edamontology.org]
is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric)
relationship: has_topic EDAM_topic:0199 ! Genetic variation

[Term]
id: EDAM_operation:0544
name: Phylogenetic species tree construction
namespace: operation
subset: operations
def: "Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison." [http://edamontology.org]
is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences)


[Term]
id: EDAM_operation:0327
name: Phylogenetic footprinting / shadowing
namespace: operation
subset: operations
def: "Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing)." [http://edamontology.org]
comment: A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.
is_a: EDAM_operation:0540 ! Phylogenetic tree construction (from molecular sequences)
relationship: has_topic EDAM_topic:0194 ! Phylogenomics

[Term]
id: EDAM_operation:0545
name: Phylogenetic tree construction (parsimony methods)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment." [http://edamontology.org]
comment: This includes evolutionary parsimony (invariants) methods.
is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric)

[Term]
id: EDAM_operation:0546
name: Phylogenetic tree construction (minimum distance methods)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances." [http://edamontology.org]
comment: This includes neighbor joining (NJ) clustering method.
is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric)

[Term]
id: EDAM_operation:0547
name: Phylogenetic tree construction (maximum likelihood and Bayesian methods)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution." [http://edamontology.org]
comment: Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.
is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric)

[Term]
id: EDAM_operation:0548
name: Phylogenetic tree construction (quartet methods)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely." [http://edamontology.org]
is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric)

[Term]
id: EDAM_operation:0549
name: Phylogenetic tree construction (AI methods)
namespace: operation
subset: operations
def: "Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms." [http://edamontology.org]
is_a: EDAM_operation:0539 ! Phylogenetic tree construction (method centric)


[Term]
id: EDAM_operation:0555
name: Phylogenetic tree construction (consensus)
namespace: operation
subset: operations
def: "Compare two or more phylogenetic trees to produce a consensus tree." [http://edamontology.org]
comment: Methods typically test for topological similarity between trees using for example a congruence index.
is_a: EDAM_operation:0325 ! Phylogenetic tree comparison
is_a: EDAM_operation:0323 ! Phylogenetic tree construction


[Term]
id: EDAM_operation:0556
name: Phylogenetic sub/super tree detection
namespace: operation
subset: operations
def: "Compare two or more phylogenetic trees to detect subtrees or supertrees." [http://edamontology.org]
is_a: EDAM_operation:0325 ! Phylogenetic tree comparison


[Term]
id: EDAM_operation:0557
name: Phylogenetic tree distances calculation
namespace: operation
subset: operations
def: "Compare two or more phylogenetic trees to calculate distances between trees." [http://edamontology.org]
is_a: EDAM_operation:0325 ! Phylogenetic tree comparison
relationship: has_output EDAM_data:1442 {min_cardinality=1} ! Phylogenetic tree report (tree distances)

[Term]
id: EDAM_operation:0558
name: Phylogenetic tree annotation
namespace: operation
subset: operations
def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org]
synonym: "CDAOAnnotattion" RELATED [http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation]
is_a: EDAM_operation:0326 ! Phylogenetic tree editing
is_a: EDAM_operation:0226 ! Annotation

[Term]
id: EDAM_operation:0328
name: Protein folding simulation
namespace: operation
subset: operations
def: "Simulate the folding of a protein." [http://edamontology.org]
is_a: EDAM_operation:2415 ! Protein folding analysis


[Term]
id: EDAM_operation:0329
name: Protein folding pathway prediction
namespace: operation
subset: operations
def: "Predict the folding pathway(s) or non-native structural intermediates of a protein." [http://edamontology.org]
is_a: EDAM_operation:2415 ! Protein folding analysis
is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein)


[Term]
id: EDAM_operation:1842
name: Proline mutation value calculation
namespace: operation
subset: operations
def: "Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein." [http://edamontology.org, WHATIF]
xref: WHATIF:ProlineMutationValue
is_a: EDAM_operation:0331 ! Protein modelling (mutation)


[Term]
id: EDAM_operation:0330
name: Protein SNP mapping
namespace: operation
subset: operations
def: "Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s)." [http://edamontology.org]
is_a: EDAM_operation:0331 ! Protein modelling (mutation)
relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)
relationship: has_topic EDAM_topic:2277 ! SNPs

[Term]
id: EDAM_operation:0559
name: Peptide immunogen prediction and optimisation
namespace: operation
subset: operations
def: "Predict and optimise peptide ligands that elicit an immunological response." [http://edamontology.org]
is_a: EDAM_operation:0252 ! Peptide immunogenicity prediction
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_output EDAM_data:1460 ! Protein structure
relationship: has_topic EDAM_topic:0150 ! Protein design
relationship: has_topic EDAM_topic:0804 ! Immunoinformatics



[Term]
id: EDAM_operation:0560
name: DNA vaccine prediction and optimisation
namespace: operation
subset: operations
def: "Predict or optimise DNA to elicit (via DNA vaccination) an immunological response." [http://edamontology.org]
is_a: EDAM_operation:3095 ! Nucleic acid design
is_a: EDAM_operation:2425 ! Optimisation and refinement
relationship: has_topic EDAM_topic:0804 ! Immunoinformatics
relationship: has_topic EDAM_topic:2953 ! Nucleic acid design

[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_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_operation:0564
name: Sequence rendering
namespace: operation
subset: operations
def: "Visualise, format or render a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 {min_cardinality=1} ! Sequence
relationship: has_output EDAM_data:2969 {min_cardinality=1} ! Sequence image

[Term]
id: EDAM_operation:2515
name: Sequence rendering (nucleic acid)
namespace: operation
subset: operations
def: "Visualise, format or render a nucleic acid sequence." [http://edamontology.org]
comment: Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
is_a: EDAM_operation:0564 ! Sequence rendering
is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid)
relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis


[Term]
id: EDAM_operation:3208 {since=1.1}
name: Genome rendering
namespace: operation
subset: operations
def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org]
synonym: "Genome browsing" EXACT [http://edamontology.org]
synonym: "Genome viewing" EXACT [http://edamontology.org]
synonym: "Genome visualisation" EXACT [http://edamontology.org]
synonym: "Genome visualization" EXACT [http://edamontology.org]
is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid)


[Term]
id: EDAM_operation:2516
name: Sequence rendering (protein)
namespace: operation
subset: operations
def: "Visualise, format or render a protein sequence." [http://edamontology.org]
comment: Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
is_a: EDAM_operation:0564 ! Sequence rendering
is_a: EDAM_operation:2447 ! Sequence processing (protein)

[Term]
id: EDAM_operation:0565
name: Sequence alignment rendering
namespace: operation
subset: operations
def: "Visualise, format or print a molecular sequence alignment." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2463 ! Sequence alignment processing
relationship: has_input EDAM_data:0863 {min_cardinality=1} ! Sequence alignment
relationship: has_output EDAM_data:1711 {min_cardinality=1} ! Sequence alignment image



[Term]
id: EDAM_operation:2452
name: Sequence cluster processing
namespace: operation
subset: operations
def: "Process (read and / or write) a sequence cluster." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:1235 {min_cardinality=0} ! Sequence cluster
relationship: has_output EDAM_data:1235 {min_cardinality=0} ! Sequence cluster
relationship: has_topic EDAM_topic:0164 ! Sequence clustering


[Term]
id: EDAM_operation:0566
name: Sequence cluster rendering
namespace: operation
subset: operations
def: "Visualise, format or render sequence clusters." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2452 ! Sequence cluster processing
relationship: has_input EDAM_data:1235 {min_cardinality=1} ! Sequence cluster

[Term]
id: EDAM_operation:0567
name: Phylogenetic tree rendering
namespace: operation
subset: operations
def: "Visualise or plot a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_operation:2443 ! Phylogenetic tree processing
is_a: EDAM_operation:0337 ! Plotting and rendering
relationship: has_output EDAM_data:0872 {min_cardinality=1} ! Phylogenetic tree


[Term]
id: EDAM_operation:0568
name: RNA secondary structure rendering
namespace: operation
subset: operations
def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2439 ! RNA secondary structure processing
relationship: has_input EDAM_data:0880 {min_cardinality=1} ! RNA secondary structure record

[Term]
id: EDAM_operation:0569
name: Protein secondary structure rendering
namespace: operation
subset: operations
def: "Render and visualise protein secondary structure." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2444 ! Protein secondary structure processing
relationship: has_input EDAM_data:0876 {min_cardinality=1} ! Protein features (secondary structure)

[Term]
id: EDAM_operation:2485
name: Helical wheel rendering
namespace: operation
subset: operations
def: "Render a helical wheel representation of protein secondary structure." [http://edamontology.org]
is_a: EDAM_operation:0569 ! Protein secondary structure rendering
relationship: has_output EDAM_data:2162 {min_cardinality=1} ! Helical wheel

[Term]
id: EDAM_operation:2486
name: Topology diagram rendering
namespace: operation
subset: operations
def: "Render a topology diagram of protein secondary structure." [http://edamontology.org]
is_a: EDAM_operation:0569 ! Protein secondary structure rendering
relationship: has_output EDAM_data:2992 ! Protein structure image

[Term]
id: EDAM_operation:2241
name: Transmembrane protein rendering
namespace: operation
subset: operations
def: "Visualise transmembrane proteins, typically the transmembrane regions within a sequence." [http://edamontology.org]
is_a: EDAM_operation:0569 ! Protein secondary structure rendering
is_a: EDAM_operation:0270 ! Transmembrane protein analysis
relationship: has_input EDAM_data:1456 {min_cardinality=1} ! Protein features (membrane regions)
relationship: has_output EDAM_data:2992 ! Protein structure image

[Term]
id: EDAM_operation:2482
name: Secondary structure processing
namespace: operation
subset: operations
def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:2081 {min_cardinality=0} ! Secondary structure
relationship: has_output EDAM_data:2081 {min_cardinality=0} ! Secondary structure
relationship: has_topic EDAM_topic:0081 ! Structure analysis


[Term]
id: EDAM_operation:2465
name: Structure processing
namespace: operation
subset: operations
! alt_id: EDAM_operation:2484
def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org]
is_a: EDAM_operation:2420 ! Analysis and processing
relationship: has_input EDAM_data:0883 {min_cardinality=0} ! Structure
relationship: has_output EDAM_data:0883 {min_cardinality=0} ! Structure
relationship: has_topic EDAM_topic:0081 ! Structure analysis

[Term]
id: EDAM_operation:0570
name: Structure rendering
namespace: operation
subset: operations
def: "Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2465 ! Structure processing
relationship: has_input EDAM_data:0883 {min_cardinality=1} ! Structure
relationship: has_output EDAM_data:1710 ! Structure image


[Term]
id: EDAM_operation:0571
name: Microarray data rendering
namespace: operation
subset: operations
def: "Visualise microarray data." [http://edamontology.org]
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2435 ! Gene expression profile processing
relationship: has_input EDAM_data:3117 {min_cardinality=1} ! Microarray hybridisation data
relationship: has_output EDAM_data:2967 {min_cardinality=1} ! Microarray image

[Term]
id: EDAM_operation:0572
name: Protein interaction network rendering
namespace: operation
subset: operations
def: "Identify and analyse networks of protein interactions." [http://edamontology.org]
is_a: EDAM_operation:3083 ! Pathway or network rendering
is_a: EDAM_operation:2445 ! Protein interaction network processing
relationship: has_input EDAM_data:1663 {min_cardinality=1} ! Pathway or network (protein-protein interaction)

[Term]
id: EDAM_operation:0573
name: Map rendering
namespace: operation
subset: operations
def: "Render and visualise a DNA map." [http://edamontology.org]
synonym: "DNA map rendering" EXACT [http://edamontology.org]
is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid)
is_a: EDAM_operation:2521 ! Map data processing
relationship: has_input EDAM_data:1274 {min_cardinality=1} ! Map


[Term]
id: EDAM_operation:3184 {since=1.1}
name: Sequence assembly rendering
namespace: operation
subset: operations
def: "Render and visualise a DNA sequence assembly." [http://edamontology.org]
synonym: "Assembly rendering" EXACT [http://edamontology.org]
synonym: "Assembly visualisation" EXACT [http://edamontology.org]
synonym: "Sequence assembly visualisation" EXACT [http://edamontology.org]
is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid)


[Term]
id: EDAM_operation:0574
name: Sequence motif rendering
namespace: operation
subset: operations
def: "Render a sequence with motifs." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0564 ! Sequence rendering


[Term]
id: EDAM_operation:0577
name: DNA linear map rendering
namespace: operation
subset: operations
def: "Draw a linear maps of DNA." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_operation:0573 ! Map rendering

[Term]
id: EDAM_operation:0578
name: DNA circular map rendering
namespace: operation
subset: operations
def: "Draw a circular maps of DNA, for example a plasmid map." [http://edamontology.org]
is_a: EDAM_operation:0573 ! Map rendering

[Term]
id: EDAM_operation:0579
name: Operon rendering
namespace: operation
subset: operations
def: "Visualise operon structure etc." [http://edamontology.org]
is_a: EDAM_operation:0573 ! Map rendering
relationship: has_topic EDAM_topic:0109 ! Gene finding


[Term]
id: EDAM_operation:0575
name: Restriction map rendering
namespace: operation
subset: operations
def: "Visualise restriction maps in DNA sequences." [http://edamontology.org]
is_a: EDAM_operation:0573 ! Map rendering
is_a: EDAM_operation:0431 ! Restriction site recognition
relationship: has_output EDAM_data:1289 ! Restriction map








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!
! Data
!


[Term]
id: EDAM_data:0005
name: Resource type
namespace: data
subset: data
def: "A type of computational resource used in bioinformatics." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}

[Term]
id: EDAM_data:2831
name: Databank
namespace: data
subset: data
def: "A flat-file (textual) data archive." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}

[Term]
id: EDAM_data:2832
name: Web portal
namespace: data
subset: data
def: "A web site providing data (web pages) on a common theme to a HTTP client." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:0581
name: Database
namespace: data
subset: data
def: "A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:0007
name: Tool
namespace: data
subset: data
def: "A bioinformatics package or tool, e.g. a standalone application or web service." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}

[Term]
id: EDAM_data:1884
name: UniProt keywords
namespace: data
subset: data
def: "A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:0831
name: MeSH vocabulary
namespace: data
subset: data
def: "Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:0832
name: HGNC vocabulary
namespace: data
subset: data
def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:0835
name: UMLS vocabulary
namespace: data
subset: data
def: "Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:2100
name: Type
namespace: data
subset: data
! alt_id: EDAM_data:2864
def: "A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values)." [http://edamontology.org]
synonym: "Type" EXACT [http://purl.org/dc/elements/1.1/type]
is_a: EDAM_data:2527 ! Parameter

[Term]
id: EDAM_data:1866
name: Map type
namespace: data
subset: data
def: "A designation of the type of map (genetic map, physical map, sequence map etc) or map set." [http://edamontology.org]
comment: Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
is_a: EDAM_data:2100 ! Type
is_a: EDAM_data:2019 ! Map attribute

[Term]
id: EDAM_data:1094
name: Sequence type
namespace: data
subset: data
def: "A label (text token) describing a type of molecular sequence." [http://edamontology.org]
comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
is_a: EDAM_data:2100 ! Type
is_a: EDAM_data:2534 ! Sequence parameter
relationship: is_identifier_of EDAM_data:2044 ! Sequence
relationship: is_identifier_of EDAM_data:0849 ! Sequence record


[Term]
id: EDAM_data:2132
name: Mutation type
namespace: data
subset: data
def: "A type of point or block mutation, including insertion, deletion, change, duplication and moves." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2100 ! Type

[Term]
id: EDAM_data:0985
name: Molecule type
namespace: data
subset: data
def: "A label (text token) describing the type a molecule." [http://edamontology.org]
comment: For example, 'Protein', 'DNA', 'RNA' etc.
example: "Protein" "DNA" "RNA"
is_a: EDAM_data:2100 ! Type

[Term]
id: EDAM_data:1122
name: Phylogenetic tree type
namespace: data
subset: data
def: "A label (text token) describing the type of a phylogenetic tree." [http://edamontology.org]
comment: For example 'nj', 'upgmp' etc.
example: "nj" "upgmp"
is_a: EDAM_data:2100 ! Type
relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree

[Term]
id: EDAM_data:2592
name: Cancer type
namespace: data
subset: data
def: "A type (represented as a string) of cancer." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2100 ! Type

[Term]
id: EDAM_data:2524
name: Protein data
namespace: data
subset: data
def: "Data concerning one or more protein 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:0896 ! Protein report

[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_data:2248
name: Schema
namespace: data
subset: data
def: "A data schema for organising or transforming data of some type." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:0843
name: Database entry
namespace: data
subset: data
def: "An entry (retrievable via URL) from a biological database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0006 ! Data


[Term]
id: EDAM_data:2767
name: Identifier with metadata
namespace: data
subset: data
def: "Basic information concerning an identifier of data (typically including the identifier itself).  For example, a gene symbol with information concerning its provenance." [http://edamontology.org]
is_a: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:2768
name: Gene symbol annotation
namespace: data
subset: data
def: "Annotation about a gene symbol." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2767 ! Identifier with metadata


[Term]
id: EDAM_data:2087
name: Molecular property
namespace: data
subset: data
def: "A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule." [http://edamontology.org]
synonym: "Physicochemical property" EXACT [http://edamontology.org]
synonym: "sequence_attribute" RELATED [SO:0000400]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:1917
name: Atomic property
namespace: data
subset: data
def: "Data for an atom (in a molecular structure)." [http://edamontology.org]
synonym: "General atomic property" EXACT [http://edamontology.org]
is_a: EDAM_data:2087 ! Molecular property

[Term]
id: EDAM_data:2050
name: Molecular property (general)
namespace: data
subset: data
def: "General data for a molecule." [http://edamontology.org]
synonym: "General molecular property" EXACT [http://edamontology.org]
is_a: EDAM_data:2087 ! Molecular property


[Term]
id: EDAM_data:2925
name: Sequence data
namespace: data
subset: data
def: "Data concerning molecular sequence(s)." [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:2044 ! Sequence
consider: EDAM_data:2955 ! Sequence report


[Term]
id: EDAM_data:2044
name: Sequence
namespace: data
subset: data
def: "One or more molecular sequences, possibly with associated annotation." [http://edamontology.org]
comment: This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records.  It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
synonym: "bio molecular sequence information" RELATED [http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation]
relationship: has_topic EDAM_topic:0080 ! Sequence analysis
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:2976
name: Protein sequence
namespace: data
subset: data
def: "One or more protein sequences, possibly with associated annotation." [http://edamontology.org]
synonym: "amino acid sequence information" RELATED [http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation]
is_a: EDAM_data:2044 ! Sequence

[Term]
id: EDAM_data:2977
name: Nucleic acid sequence
namespace: data
subset: data
def: "One or more nucleic acid sequences, possibly with associated annotation." [http://edamontology.org]
synonym: "nucleotide sequence information" RELATED [http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation]
is_a: EDAM_data:2044 ! Sequence

[Term]
id: EDAM_data:2955
name: Sequence report
namespace: data
subset: data
def: "An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata)." [http://edamontology.org]
synonym: "Sequence-derived report" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:0855
name: Sequence metadata
namespace: data
subset: data
def: "Basic or general information concerning molecular sequences." [http://edamontology.org]
comment: This is used for such things as a report including the sequence identifier, type and length.
is_a: EDAM_data:1254 ! Sequence property
is_a: EDAM_data:2955 ! Sequence report
is_a: EDAM_data:2337 ! Metadata

[Term]
id: EDAM_data:2522
name: Map data
namespace: data
subset: data
def: "Data concerning a map of molecular sequence(s)." [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:1274 ! Map
consider: EDAM_data:2019 ! Map attribute


[Term]
id: EDAM_data:1274
name: Map
namespace: data
subset: data
def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org]
synonym: "DNA map" EXACT [http://edamontology.org]
relationship: has_topic EDAM_topic:0102 ! Mapping
is_a: EDAM_data:3031 ! Core data

[Term]
id: EDAM_data:1864
name: Map set
namespace: data
subset: data
def: "Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped." [http://edamontology.org]
xref: Moby:GCP_CorrelatedMapSet
xref: Moby:GCP_CorrelatedLinkageMapSet
is_a: EDAM_data:2019 ! Map attribute


[Term]
id: EDAM_data:2019
name: Map attribute
namespace: data
subset: data
def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:0102 ! Mapping


[Term]
id: EDAM_data:2080
name: Database hits
namespace: data
subset: data
def: "A report of hits from searching a database of some type." [http://edamontology.org]
is_a: EDAM_data:2093 ! Data reference

[Term]
id: EDAM_data:0860
name: Sequence signature
namespace: data
subset: data
def: "A classifier of sequences such as a sequence motif, profile or other diagnostic element." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1353 ! Sequence motif
consider: EDAM_data:1354 ! Sequence profile

[Term]
id: EDAM_data:2981
name: Sequence motif data
namespace: data
subset: data
def: "Data concerning specific or conserved pattern in molecular sequences." [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:1353 ! Sequence motif

[Term]
id: EDAM_data:1353
name: Sequence motif
namespace: data
subset: data
def: "Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0158 ! Sequence motifs

[Term]
id: EDAM_data:2762
name: Sequence motif metadata
namespace: data
subset: data
def: "Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:0158 ! Sequence motifs

[Term]
id: EDAM_data:2982
name: Sequence profile data
namespace: data
subset: data
def: "Data concerning models representing a (typically multiple) sequence alignment." [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:1354 ! Sequence profile

[Term]
id: EDAM_data:1354
name: Sequence profile
namespace: data
subset: data
def: "Some type of statistical model representing a (typically multiple) sequence alignment." [http://edamontology.org]
synonym: "sequence profile" EXACT [http://semanticscience.org/resource/SIO_010531]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs

[Term]
id: EDAM_data:2788
name: Sequence profile metadata
namespace: data
subset: data
def: "Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs

[Term]
id: EDAM_data:1355
name: Protein signature
namespace: data
subset: data
def: "An entry (sequence classifier and associated data) from the InterPro database." [http://edamontology.org]
synonym: "InterPro entry" EXACT [http://edamontology.org]
is_a: EDAM_data:0907 ! Protein family

[Term]
id: EDAM_data:2161
name: Sequence similarity plot
namespace: data
subset: data
def: "A plot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org]
is_a: EDAM_data:0867 ! Sequence alignment report

[Term]
id: EDAM_data:0862
name: Dotplot
namespace: data
subset: data
def: "A dotplot of sequence similarities identified from word-matching or character comparison." [http://edamontology.org]
is_a: EDAM_data:2161 ! Sequence similarity plot

[Term]
id: EDAM_data:2539
name: Alignment data
namespace: data
subset: data
def: "Data concerning an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  This includes entities derived from sequences and structures such as motifs and profiles.
is_obsolete: true !{since=beta13}
consider: EDAM_data:1916 ! Alignment
consider: EDAM_data:2083 ! Alignment report


[Term]
id: EDAM_data:1916
name: Alignment
namespace: data
subset: data
def: "An alignment of molecular sequences, structures or profiles derived from them." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data

[Term]
id: EDAM_data:2083
name: Alignment report
namespace: data
subset: data
def: "An informative report about a molecular alignment of some type, including alignment-derived data or metadata." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:2048 ! Report

[Term]
id: EDAM_data:2711
name: Genome metadata
namespace: data
subset: data
def: "Provenance metadata or other general information concerning a genome as a whole." [http://edamontology.org]
is_a: EDAM_data:0855 ! Sequence metadata


[Term]
id: EDAM_data:0867
name: Sequence alignment report
namespace: data
subset: data
def: "An informative report of molecular sequence alignment-derived data or metadata." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:2083 ! Alignment report



[Term]
id: EDAM_data:3181 {since=1.1}
name: Sequence assembly report
namespace: data
subset: data
def: "An informative report about a DNA sequence assembly." [http://edamontology.org]
is_a: EDAM_data:2955 ! Sequence report


[Term]
id: EDAM_data:2598
name: Secondary structure alignment metadata
namespace: data
subset: data
def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2083 ! Alignment report

[Term]
id: EDAM_data:0879
name: Secondary structure alignment metadata (protein)
namespace: data
subset: data
def: "An informative report on protein secondary structure alignment-derived data or metadata." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2083 ! Alignment report


[Term]
id: EDAM_data:0882
name: Secondary structure alignment metadata (RNA)
namespace: data
subset: data
def: "An informative report of RNA secondary structure alignment-derived data or metadata." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2083 ! Alignment report


[Term]
id: EDAM_data:2082
name: Matrix
namespace: data
subset: data
def: "An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:3031 ! Core data

[Term]
id: EDAM_data:2855
name: Distance matrix
namespace: data
subset: data
def: "A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity." [http://edamontology.org]
is_a: EDAM_data:2082 ! Matrix

[Term]
id: EDAM_data:0870
name: Sequence distance matrix
namespace: data
subset: data
def: "A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation." [http://edamontology.org]
comment: Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.
synonym: "Phylogenetic distance matrix" EXACT [http://edamontology.org]
xref: Moby:phylogenetic_distance_matrix
is_a: EDAM_data:2855 ! Distance matrix

[Term]
id: EDAM_data:2856
name: Structural distance matrix
namespace: data
subset: data
def: "Distances (values representing similarity) between a group of molecular structures." [http://edamontology.org]
is_a: EDAM_data:2855 ! Distance matrix


[Term]
id: EDAM_data:2523
name: Phylogenetic raw data
namespace: data
subset: data
def: "Data concerning phylogeny, typically of molecular sequences." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Phylogenetic data" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:0871
name: Phylogenetic character data
namespace: data
subset: data
def: "Data from which a phylogenetic tree may be generated." [http://edamontology.org]
is_a: EDAM_data:2523 ! Phylogenetic raw data
synonym: "Character" RELATED [http://www.evolutionaryontology.org/cdao.owl#Character]
! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments

[Term]
id: EDAM_data:0872
name: Phylogenetic tree
namespace: data
subset: data
def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [http://edamontology.org]
comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.
synonym: "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree]
xref: Moby:Tree
xref: Moby:phylogenetic_tree
xref: Moby:myTree
relationship: has_topic EDAM_topic:0084 ! Phylogenetics
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:1438
name: Phylogenetic tree report
namespace: data
subset: data
! alt_id: EDAM_data:0873
def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Phylogenetic tree-derived report" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:0874
name: Comparison matrix
namespace: data
subset: data
def: "Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison." [http://edamontology.org]
comment: The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).
synonym: "Substitution matrix" EXACT [http://edamontology.org]
is_a: EDAM_data:2082 ! Matrix


[Term]
id: EDAM_data:2053
name: Structural data
namespace: data
subset: data
def: "Data concerning molecular structural data." [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:0883 ! Structure
consider: EDAM_data:2085 ! Structure report


[Term]
id: EDAM_data:2085
name: Structure report
namespace: data
subset: data
def: "An informative report on general information, properties or features of one or more molecular tertiary (3D) structures." [http://edamontology.org]
synonym: "Structure-derived report" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report

[Term]
id: EDAM_data:2973
name: Secondary structure data
namespace: data
subset: data
def: "Data concerning molecular secondary structure data." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2081 ! Secondary structure
consider: EDAM_data:2881 ! Secondary structure report


[Term]
id: EDAM_data:2881
name: Secondary structure report
namespace: data
subset: data
def: "An informative report on general information, properties or features of one or more molecular secondary structures." [http://edamontology.org]
synonym: "Secondary structure-derived report" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:2956
name: Protein secondary structure report
namespace: data
subset: data
def: "An informative report about the properties or features of one or more protein secondary structures." [http://edamontology.org]
is_a: EDAM_data:2881 ! Secondary structure report

[Term]
id: EDAM_data:1494
name: Structural transformation matrix
namespace: data
subset: data
def: "Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures." [http://edamontology.org]
is_a: EDAM_data:2082 ! Matrix

[Term]
id: EDAM_data:0887
name: Structure alignment report
namespace: data
subset: data
def: "An informative report on molecular tertiary structure alignment-derived data." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:2083 ! Alignment report

[Term]
id: EDAM_data:0889
name: Structural (3D) profile
namespace: data
subset: data
def: "Some type of structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org]
synonym: "3D profile" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles

[Term]
id: EDAM_data:0892
name: Protein sequence-structure scoring matrix
namespace: data
subset: data
def: "Matrix of values used for scoring sequence-structure compatibility." [http://edamontology.org]
is_a: EDAM_data:2082 ! Matrix

[Term]
id: EDAM_data:2528
name: Molecular data
namespace: data
subset: data
def: "Data concerning a specific type of molecule." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Molecule-specific data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2529 ! Molecule report


[Term]
id: EDAM_data:2599
name: Molecular interaction
namespace: data
subset: data
def: "Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules)." [http://edamontology.org]
synonym: "Molecular interaction data" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:2601
name: Small molecule data
namespace: data
subset: data
def: "Data concerning one or more small 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:0962 ! Small molecule annotation

[Term]
id: EDAM_data:2016
name: Amino acid property
namespace: data
subset: data
def: "Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids." [http://edamontology.org]
synonym: "Amino acid data" EXACT [http://edamontology.org]
is_a: EDAM_data:2087 ! Molecular property

[Term]
id: EDAM_data:2979
name: Peptide property
namespace: data
subset: data
def: "Data concerning small peptides." [http://edamontology.org]
synonym: "Peptide data" EXACT [http://edamontology.org]
is_a: EDAM_data:2087 ! Molecular property


[Term]
id: EDAM_data:0895
name: Peptide annotation
namespace: data
subset: data
def: "An informative report about a specific peptide." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation
is_a: EDAM_data:2979 ! Peptide property
relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids


[Term]
id: EDAM_data:2399
name: Gene annotation (transcript)
namespace: data
subset: data
! alt_id: EDAM_data:2703
def: "An informative report on a specific gene transcript, clone or EST." [http://edamontology.org]
synonym: "Gene transcript annotation" EXACT [http://edamontology.org]
synonym: "Gene annotation (clone or EST)" EXACT [http://edamontology.org]
is_a: EDAM_data:0916 ! Gene annotation


[Term]
id: EDAM_data:0896
name: Protein report
namespace: data
subset: data
def: "An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data." [http://edamontology.org]
synonym: "Gene product annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2529 ! Molecule report
relationship: has_topic EDAM_topic:0078 ! Protein analysis


[Term]
id: EDAM_data:0897
name: Protein property
namespace: data
subset: data
def: "A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model." [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: "Protein physicochemical property" EXACT [http://edamontology.org]
is_a: EDAM_data:0896 ! Protein report
is_a: EDAM_data:2087 ! Molecular property


[Term]
id: EDAM_data:1537
name: Protein structure report
namespace: data
subset: data
def: "Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains." [http://edamontology.org]
! alt_id: EDAM_data:0898
! alt_id: EDAM_data:1538
! alt_id: EDAM_data:2377
synonym: "Protein structure report (domain)" EXACT [http://edamontology.org]
synonym: "Protein structure-derived report" EXACT [http://edamontology.org]
synonym: "Protein structural property" EXACT [http://edamontology.org]
synonym: "Protein report (structure)" EXACT [http://edamontology.org]
synonym: "Protein property (structural)" EXACT [http://edamontology.org]
is_a: EDAM_data:0896 ! Protein report
is_a: EDAM_data:2085 ! Structure report


! [Term] born obsolete
! id: EDAM_data:3151 {since=beta13}
! name: Protein property (physicochemical)
! namespace: data
! subset: data
! def: "A report of primarily non-positional data describing intrinsic physicochemical properties of a protein molecule." [http://edamontology.org]
! synonym: "Protein physicochemical property" EXACT [http://edamontology.org]
! is_obsolete: true !{since=beta13}
! consider: EDAM_data:0897 ! Protein property


! [Term] born obsolete
! id: EDAM_data:3152 {since=beta13}
! name: Protein property (sequence)
! namespace: data
! subset: data
! def: "A non-positional property of a protein sequence." [http://edamontology.org]
! synonym: "Protein sequence property" EXACT [http://edamontology.org]
! is_obsolete: true !{since=beta13}
! consider: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:2313
name: Carbohydrate structure report
namespace: data
subset: data
def: "Annotation on or information derived from one or more specific carbohydrate 3D structure(s)." [http://edamontology.org]
is_a: EDAM_data:2085 ! Structure report

[Term]
id: EDAM_data:2879
name: Lipid structure report
namespace: data
subset: data
def: "Annotation on or information derived from one or more specific lipid 3D structure(s)." [http://edamontology.org]
is_a: EDAM_data:2085 ! Structure report



[Term]
id: EDAM_data:2987
name: Classification
namespace: data
subset: data
def: "Data concerning a classification of molecular sequences, structures or other entities." [http://edamontology.org]
comment: This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
synonym: "Classification data" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:2829 ! Ontologies, nomenclature and classification

[Term]
id: EDAM_data:3028
name: Taxonomy
namespace: data
subset: data
def: "Data concerning the classification, identification and naming of organisms." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Taxonomic data" EXACT [http://edamontology.org]
is_a: EDAM_data:2987 ! Classification
relationship: has_topic EDAM_topic:0637 ! Taxonomy



[Term]
id: EDAM_data:2986
name: Nucleic acid classification
namespace: data
subset: data
def: "Data concerning the classification of nucleic acid sequences or structures." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Nucleic acid classification data" EXACT [http://edamontology.org]
is_a: EDAM_data:2084 ! Nucleic acid report
is_a: EDAM_data:2987 ! Classification
relationship: has_topic EDAM_topic:0722 ! Nucleic acid classification

[Term]
id: EDAM_data:2980
name: Protein classification
namespace: data
subset: data
def: "Data concerning the classification of protein sequences or structures." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Protein classification data" EXACT [http://edamontology.org]
is_a: EDAM_data:0896 ! Protein report
is_a: EDAM_data:2987 ! Classification
relationship: has_topic EDAM_topic:0595 ! Protein classification

[Term]
id: EDAM_data:0900
name: Protein domain classification
namespace: data
subset: data
def: "Data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org]
is_a: EDAM_data:2980 ! Protein classification
relationship: has_topic EDAM_topic:0736 ! Protein domains and folds

[Term]
id: EDAM_data:3101 {since=beta13}
name: Protein domain classification node
namespace: data
subset: data
def: "A node from a classification of protein structural domain(s)." [http://edamontology.org]
is_a: EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_data:0906
name: Protein interaction
namespace: data
subset: data
def: "An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand." [http://edamontology.org]
synonym: "Protein report (interaction)" EXACT [http://edamontology.org]
is_a: EDAM_data:2599 ! Molecular interaction
is_a: EDAM_data:0896 ! Protein report
relationship: has_topic EDAM_topic:0128 ! Protein interactions

[Term]
id: EDAM_data:0907
name: Protein family
namespace: data
subset: data
def: "An informative report on a specific protein family or other group of classified proteins." [http://edamontology.org]
synonym: "Protein family annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2980 ! Protein classification
relationship: has_topic EDAM_topic:0724 ! Protein families


[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:2978
name: Reaction data
namespace: data
subset: data
! alt_id: EDAM_data:0908
def: "Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Reaction annotation" EXACT [http://edamontology.org]
synonym: "Enzyme kinetics annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data



[Term]
id: EDAM_data:2024
name: Enzyme kinetics data
namespace: data
subset: data
def: "Data concerning chemical reaction(s) catalysed by enzyme(s)." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:2978 ! Reaction data

[Term]
id: EDAM_data:0911
name: Nucleotide base annotation
namespace: data
subset: data
def: "An informative report about a specific nucleotide base." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation

[Term]
id: EDAM_data:2116
name: Nucleic acid features (codon)
namespace: data
subset: data
def: "An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1276 ! Nucleic acid features

[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_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:2086
name: Nucleic acid structure report
namespace: data
subset: data
! alt_id: EDAM_data:0913
def: "A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s)." [http://edamontology.org]
comment: This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.
synonym: "Nucleic acid structural property" EXACT [http://edamontology.org]
synonym: "Nucleic acid property (structural)" EXACT [http://edamontology.org]
is_a: EDAM_data:0912 ! Nucleic acid property
is_a: EDAM_data:2085 ! Structure report



[Term]
id: EDAM_data:2927
name: Codon usage data
namespace: data
subset: data
def: "Data concerning codon usage." [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:1597 ! Codon usage table
consider: EDAM_data:0914 ! Codon usage report


[Term]
id: EDAM_data:1597
name: Codon usage table
namespace: data
subset: data
def: "Table of codon usage data calculated from one or more nucleic acid sequences." [http://edamontology.org]
comment: A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0107 ! Codon usage analysis

[Term]
id: EDAM_data:0914
name: Codon usage report
namespace: data
subset: data
def: "Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM_data:2048 ! Report
relationship: has_topic EDAM_topic:0107 ! Codon usage analysis

[Term]
id: EDAM_data:2603
name: Microarray data
namespace: data
subset: data
! alt_id: EDAM_data:2541
def: "Image or hybridisation data for a microarray, typically a study of gene expression." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  See also EDAM_data:0931 ! Experiment annotation (microarray)
synonym: "Gene expression data" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data



[Term]
id: EDAM_data:3110 {since=beta13}
name: Raw microarray data
namespace: data
subset: data
def: "Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment." [http://edamontology.org]
comment: Such data as found in Affymetrix CEL or GPR files.
is_a: EDAM_data:3117 ! Microarray hybridisation data
is_a: EDAM_data:3108 ! Experimental measurement


[Term]
id: EDAM_data:3111 {since=beta13}
name: Processed microarray data
namespace: data
subset: data
! alt_id: EDAM_data:0929
def: "Data generated from processing and analysis of probe set data from a microarray experiment." [http://edamontology.org]
comment: Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.
synonym: "Microarray probe set data" EXACT [http://edamontology.org]
synonym: "Gene expression report" EXACT [http://edamontology.org]
synonym: "Gene annotation (expression)" EXACT [http://edamontology.org]
is_a: EDAM_data:3117 ! Microarray hybridisation data
is_a: EDAM_data:0928 ! Gene expression profile
relationship: has_topic EDAM_topic:0200 ! Microarrays


[Term]
id: EDAM_data:3117 {since=beta13}
name: Microarray hybridisation data
namespace: data
subset: data
def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org]
is_a: EDAM_data:2603 ! Microarray data
relationship: has_topic EDAM_topic:0200 ! Microarrays

[Term]
id: EDAM_data:3112 {since=beta13}
name: Normalised microarray data
namespace: data
subset: data
def: "The final processed (normalised) data for a set of hybridisations in a microarray experiment." [http://edamontology.org]
comment: This combines data from all hybridisations.
synonym: "Gene expression matrix" EXACT [http://edamontology.org]
synonym: "Gene expression data matrix" EXACT [http://edamontology.org]
is_a: EDAM_data:3117 ! Microarray hybridisation data

[Term]
id: EDAM_data:3113 {since=beta13}
name: Sample annotation
namespace: data
subset: data
def: "Annotation on a biological sample, for example experimental factors and their values." [http://edamontology.org]
comment: This might include compound and dose in a dose response experiment.
is_a: EDAM_data:0931 ! Experiment annotation (microarray)






[Term]
id: EDAM_data:3115 {since=beta13}
name: Microarray annotation
namespace: data
subset: data
def: "Annotation on the array itself used in a microarray experiment." [http://edamontology.org]
comment: This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.
is_a: EDAM_data:0931 ! Experiment annotation (microarray)


[Term]
id: EDAM_data:3116 {since=beta13}
name: Microarray protocol annotation
namespace: data
subset: data
def: "Annotation on laboratory and/or data processing protocols used in an microarray experiment." [http://edamontology.org]
comment: This might describe e.g. the normalisation methods used to process the raw data.
is_a: EDAM_data:0931 ! Experiment annotation (microarray)


[Term]
id: EDAM_data:2763
name: Locus annotation
namespace: data
subset: data
def: "An informative report on a particular locus." [http://edamontology.org]
synonym: "Locus report" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0916 ! Gene annotation

[Term]
id: EDAM_data:0916
name: Gene annotation
namespace: data
subset: data
! alt_id: EDAM_data:2394
! alt_id: EDAM_data:2361
def: "An informative report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org]
comment: This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).
synonym: "Gene report" EXACT [http://edamontology.org]
synonym: "Gene annotation (functional)" EXACT [http://edamontology.org]
xref: Moby:gene
xref: Moby:GeneInfo
xref: Moby_namespace:Human_Readable_Description
is_a: EDAM_data:1276 ! Nucleic acid features
relationship: has_topic EDAM_topic:0623 ! Genes, gene family or system

[Term]
id: EDAM_data:3148 {since=beta13}
name: Gene family annotation
namespace: data
subset: data
def: "An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene." [http://edamontology.org]
is_a: EDAM_data:2986 ! Nucleic acid classification
is_a: EDAM_data:0916 ! Gene annotation


[Term]
id: EDAM_data:0918
name: Nucleic acid features (variation)
namespace: data
subset: data
def: "A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms." [http://edamontology.org]
synonym: "Sequence variation annotation" EXACT [http://edamontology.org]
synonym: "sequence_alteration" RELATED [SO:0001059]
is_a: EDAM_data:3122 ! Nucleic acid features (difference and change)
relationship: has_topic EDAM_topic:0199 ! Genetic variation


[Term]
id: EDAM_data:0919
name: Gene annotation (chromosome)
namespace: data
subset: data
def: "An informative report on a specific chromosome." [http://edamontology.org]
comment: This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
is_a: EDAM_data:0916 ! Gene annotation
relationship: has_topic EDAM_topic:0624 ! Chromosomes

[Term]
id: EDAM_data:2602
name: Genotype and phenotype data
namespace: data
subset: data
def: "Data concerning a particular genotype, phenotype or a genotype / phenotype relation." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0920 ! Genotype/phenotype annotation


[Term]
id: EDAM_data:0920
name: Genotype/phenotype annotation
namespace: data
subset: data
! alt_id: EDAM_data:2890
def: "An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes." [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:2531
name: Experiment annotation
namespace: data
subset: data
def: "Annotation on a wet lab experiment, such as experimental conditions." [http://edamontology.org]
is_a: EDAM_data:2048 ! Report

! [Term] born obsolete
! id: EDAM_data:3109 {since=beta13}
! name: Experimental measurement annotation
! namespace: data
! subset: data
! def: "Annotation on the result of a wet lab experiment." [http://edamontology.org]
! is_obsolete: true !{since=beta13}
! consider: EDAM_data:3108 ! Experimental measurement
! consider: EDAM_data:2531 ! Experiment annotation




[Term]
id: EDAM_data:2381
name: Experiment annotation (genotype)
namespace: data
subset: data
def: "Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods." [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation


[Term]
id: EDAM_data:3231 {since=1.1}
name: Experiment annotation (GWAS)
namespace: data
subset: data
def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org]
synonym: "Experiment annotation (genome-wide association study)" EXACT [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation




[Term]
id: EDAM_data:0925
name: Sequence assembly
namespace: data
subset: data
def: "An assembly of fragments of a (typically genomic) DNA sequence." [http://edamontology.org]
comment: Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.
synonym: "Sequence assembly" EXACT [http://en.wikipedia.org/wiki/Sequence_assembly]
synonym: "sequence_assembly" EXACT [SO:0000353]
synonym: "assembly" NARROW [SO:0001248] {note="Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'."}
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)

[Term]
id: EDAM_data:2028
name: Experimental data
namespace: data
subset: data
def: "Raw data from or annotation on laboratory experiments." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Experimental measurement data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:3108 ! Experimental measurement
consider: EDAM_data:2531 ! Experiment annotation

[Term]
id: EDAM_data:3108 {since=beta13}
name: Experimental measurement
namespace: data
subset: data
def: "Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Raw experimental data" EXACT [http://edamontology.org]
synonym: "Experimental measurement data" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data




[Term]
id: EDAM_data:2042
name: Evidence
namespace: data
subset: data
def: "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter

[Term]
id: EDAM_data:0941
name: Electron microscopy model
namespace: data
subset: data
def: "Annotation on a structural 3D model (volume map) from electron microscopy." [http://edamontology.org]
comment: This might include the location in the model of the known features of a particular macromolecule.
is_a: EDAM_data:0940 ! Electron microscopy volume map
relationship: has_topic EDAM_topic:2226 ! Structure determination

[Term]
id: EDAM_data:2971
name: Workflow data
namespace: data
subset: data
def: "Data concerning a computational workflow." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0949 ! Workflow metadata
consider: EDAM_data:2972 ! Workflow


[Term]
id: EDAM_data:0949
name: Workflow metadata
namespace: data
subset: data
def: "Basic information, annotation or documentation concerning a workflow (but not the workflow itself)." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
! relationship: has_topic EDAM_topic:0769 ! Workflows


[Term]
id: EDAM_data:2972
name: Workflow
namespace: data
subset: data
def: "A computational workflow." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
! relationship: has_topic EDAM_topic:0769 ! Workflows


[Term]
id: EDAM_data:0950
name: Biological model
namespace: data
subset: data
def: "A biological model which can be represented in mathematical terms." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0771 ! Biological models

[Term]
id: EDAM_data:2983
name: Pathway or network data
namespace: data
subset: data
def: "Data concerning a specific biological pathway or network." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2600 ! Pathway or network
consider: EDAM_data:2984 ! Pathway or network report


[Term]
id: EDAM_data:2984
name: Pathway or network report
namespace: data
subset: data
def: "An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation." [http://edamontology.org]
is_a: EDAM_data:2048 ! Report
relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models

[Term]
id: EDAM_data:2600
name: Pathway or network
namespace: data
subset: data
def: "Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network)." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models


[Term]
id: EDAM_data:1883
name: Annotated URI
namespace: data
subset: data
def: "A URI along with annotation describing the data found at the address." [http://edamontology.org]
xref: Moby:DescribedLink
is_a: EDAM_data:2337 ! Metadata
is_a: EDAM_data:2093 ! Data reference


[Term]
id: EDAM_data:0954
name: Database cross-mapping
namespace: data
subset: data
def: "A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases." [http://edamontology.org]
comment: The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.
is_a: EDAM_data:2093 ! Data reference


[Term]
id: EDAM_data:2872
name: ID list
namespace: data
subset: data
def: "A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data." [http://edamontology.org]
is_a: EDAM_data:2093 ! Data reference

[Term]
id: EDAM_data:2765
name: Term ID list
namespace: data
subset: data
def: "One or more terms from one or more controlled vocabularies which are annotations on an entity." [http://edamontology.org]
comment: The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.
is_a: EDAM_data:2872 ! ID list

[Term]
id: EDAM_data:1111
name: EMBOSS listfile
namespace: data
subset: data
def: "List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile)." [http://edamontology.org]
is_a: EDAM_data:2872 ! ID list


[Term]
id: EDAM_data:2093
name: Data reference
namespace: data
subset: data
def: "Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology." [http://edamontology.org]
comment: A list of database accessions or identifiers are usually included.
is_a: EDAM_data:3031 ! Core data

[Term]
id: EDAM_data:2540
name: Data index data
namespace: data
subset: data
def: "Data concerning an index of data." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Database index" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0955 ! Data index
consider: EDAM_data:0956 ! Data index report

[Term]
id: EDAM_data:0955
name: Data index
namespace: data
subset: data
def: "An index of data of biological relevance." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0220 ! Data processing and validation


[Term]
id: EDAM_data:3210 {since=1.1}
name: Genome index
namespace: data
subset: data
def: "An index of a genome sequence." [http://edamontology.org]
comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
is_a: EDAM_data:0955 ! Data index



[Term]
id: EDAM_data:0956
name: Data index report
namespace: data
subset: data
def: "A report of an analysis of an index of biological data." [http://edamontology.org]
synonym: "Database index annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report
relationship: has_topic EDAM_topic:0220 ! Data processing and validation


[Term]
id: EDAM_data:2048
name: Report
namespace: data
subset: data
! alt_id: EDAM_data:0969
! alt_id: EDAM_data:3037 {since=beta13} ! Not released
def: "A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.  'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described.  This includes metadata on the origin, source, history, ownership or location of some thing.
synonym: "Document" EXACT [http://edamontology.org]
synonym: "Text" EXACT [http://edamontology.org]
synonym: "document" RELATED [http://semanticscience.org/resource/SIO_000148] ! Related external synonym in EDAM without a note is usually almost exact.
is_a: EDAM_data:0006 ! Data


[Term]
id: EDAM_data:1772
name: Score or penalty
namespace: data
subset: data
! alt_id: EDAM_data:2138
def: "A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty)." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:2529
name: Molecule report
namespace: data
subset: data
def: "An informative report on a specific molecule." [http://edamontology.org]
synonym: "Molecular report" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report

[Term]
id: EDAM_data:0962
name: Small molecule annotation
namespace: data
subset: data
def: "An informative report on a specific chemical compound." [http://edamontology.org]
synonym: "Chemical compound annotation" EXACT [http://edamontology.org]
synonym: "Small molecule report" EXACT [http://edamontology.org]
is_a: EDAM_data:2085 ! Structure report
is_a: EDAM_data:2529 ! Molecule report
relationship: has_topic EDAM_topic:0154 ! Small molecules


[Term]
id: EDAM_data:0963
name: Cell line annotation
namespace: data
subset: data
def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [http://edamontology.org]
synonym: "Organism strain data" EXACT [http://edamontology.org]
is_a: EDAM_data:2530 ! Organism annotation

[Term]
id: EDAM_data:2530
name: Organism annotation
namespace: data
subset: data
def: "An informative report on a specific organism." [http://edamontology.org]
is_a: EDAM_data:2048 ! Report

[Term]
id: EDAM_data:2307
name: Virus annotation
namespace: data
subset: data
def: "An informative report on a specific virus." [http://edamontology.org]
is_a: EDAM_data:2530 ! Organism annotation

[Term]
id: EDAM_data:2395
name: Fungi annotation
namespace: data
subset: data
def: "An informative report on a specific fungus." [http://edamontology.org]
is_a: EDAM_data:2530 ! Organism annotation

[Term]
id: EDAM_data:0964
name: Scent annotation
namespace: data
subset: data
def: "An informative report about a specific scent." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation



[Term]
id: EDAM_data:2968
name: Image
namespace: data
subset: data
! alt_id: EDAM_data:0965
def: "Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type." [http://edamontology.org]
synonym: "visual entity" BROAD [http://semanticscience.org/resource/SIO_000079]
synonym: "image" NARROW [http://semanticscience.org/resource/SIO_000081]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:2884
name: Plot
namespace: data
subset: data
def: "Biological data that is plotted as a graph of some type." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2968 ! Image

[Term]
id: EDAM_data:2353
name: Ontological data
namespace: data
subset: data
def: "Data concerning an ontology." [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:2223 ! Ontology metadata
consider: EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:2849
name: Abstract
namespace: data
subset: data
def: "An abstract of a scientific article." [http://edamontology.org]
is_a: EDAM_data:2857 ! Article metadata


[Term]
id: EDAM_data:0970
name: Bibliographic reference
namespace: data
subset: data
def: "Bibliographic data that uniquely identifies a scientific article, book or other published material." [http://edamontology.org]
comment: A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.
synonym: "Reference" EXACT [http://edamontology.org]
synonym: "Citation" EXACT [http://edamontology.org]
xref: Moby:GCP_SimpleCitation
xref: Moby:Publication
is_a: EDAM_data:2857 ! Article metadata
is_a: EDAM_data:2093 ! Data reference


[Term]
id: EDAM_data:2526
name: Article data
namespace: data
subset: data
def: "Data concerning the scientific literature." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0971 ! Article

[Term]
id: EDAM_data:0971
name: Article
namespace: data
subset: data
def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:3068 ! Literature and reference

[Term]
id: EDAM_data:2857
name: Article metadata
namespace: data
subset: data
def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org]
is_a: EDAM_data:2954 ! Article report
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:3068 ! Literature and reference


[Term]
id: EDAM_data:2954
name: Article report
namespace: data
subset: data
def: "Data concerning or derived from the analysis of a scientific article." [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:0972
name: Text mining report
namespace: data
subset: data
def: "An abstract of the results of text mining." [http://edamontology.org]
comment: A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.
is_a: EDAM_data:2954 ! Article report



[Term]
id: EDAM_data:2143
name: EMBOSS report
namespace: data
subset: data
def: "An application report generated by the EMBOSS suite." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2048 ! Report

[Term]
id: EDAM_data:2176
name: Cardinality
namespace: data
subset: data
def: "The number of a certain thing." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:2527
name: Parameter
namespace: data
subset: data
! alt_id: EDAM_data:2029
! alt_id: EDAM_data:1773
! alt_id: EDAM_data:0961
def: "Typically a simple numerical or string value that controls the operation of a tool." [http://edamontology.org]
synonym: "Parameter or primitive" EXACT [http://edamontology.org]
synonym: "Tool parameter" EXACT [http://edamontology.org]
synonym: "Tool-specific parameter" EXACT [http://edamontology.org]
synonym: "Parameter" EXACT [http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter]
synonym: "parameter" EXACT [http://semanticscience.org/resource/SIO_000144] {note="Slightly narrower in the sense of changing the characteristics of a system/function."}
is_a: EDAM_data:0006 ! Data


[Term]
id: EDAM_data:2190
name: Sequence checksum
namespace: data
subset: data
def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing." [http://edamontology.org]
synonym: "Hash code" EXACT [http://edamontology.org]
synonym: "Hash sum" EXACT [http://edamontology.org]
synonym: "Hash" EXACT [http://edamontology.org]
synonym: "Hash value" EXACT [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter
is_a: EDAM_data:0855 ! Sequence metadata


[Term]
id: EDAM_data:2192
name: Error
namespace: data
subset: data
def: "Data on an error generated by computer system or tool." [http://edamontology.org]
is_a: EDAM_data:0959 ! Job metadata

[Term]
id: EDAM_data:2249
name: DTD
namespace: data
subset: data
def: "A DTD (document type definition)." [http://edamontology.org]
is_a: EDAM_data:2248 ! Schema


[Term]
id: EDAM_data:2250
name: XML Schema
namespace: data
subset: data
def: "An XML Schema." [http://edamontology.org]
synonym: "XSD" EXACT [http://edamontology.org]
is_a: EDAM_data:2248 ! Schema


[Term]
id: EDAM_data:2251
name: Relax-NG schema
namespace: data
subset: data
def: "A relax-NG schema." [http://edamontology.org]
is_a: EDAM_data:2248 ! Schema


[Term]
id: EDAM_data:2252
name: XSLT stylesheet
namespace: data
subset: data
def: "An XSLT stylesheet." [http://edamontology.org]
is_a: EDAM_data:2248 ! Schema


[Term]
id: EDAM_data:1743
name: Atomic coordinate
namespace: data
subset: data
def: "Cartesian coordinate of an atom (in a molecular structure)." [http://edamontology.org]
synonym: "Cartesian coordinate" EXACT [http://edamontology.org]
is_a: EDAM_data:1917 ! Atomic property


[Term]
id: EDAM_data:1857
name: Atomic occupancy
namespace: data
subset: data
def: "The fraction of an atom type present at a site in a molecular structure." [http://edamontology.org]
comment: The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.
xref: WHATIF: PDBx_occupancy
is_a: EDAM_data:1917 ! Atomic property


[Term]
id: EDAM_data:1858
name: Isotropic B factor
namespace: data
subset: data
def: "Isotropic B factor (atomic displacement parameter) for an atom from a PDB file." [http://edamontology.org]
xref: WHATIF: PDBx_B_iso_or_equiv
is_a: EDAM_data:1917 ! Atomic property

[Term]
id: EDAM_data:1744
name: Atomic x coordinate
namespace: data
subset: data
def: "Cartesian x coordinate of an atom (in a molecular structure)." [http://edamontology.org]
synonym: "Cartesian x coordinate" EXACT [http://edamontology.org]
xref: WHATIF: PDBx_Cartn_x
is_a: EDAM_data:1743 ! Atomic coordinate
! _atom_site.Cartn_x in PDBML

[Term]
id: EDAM_data:1745
name: Atomic y coordinate
namespace: data
subset: data
def: "Cartesian y coordinate of an atom (in a molecular structure)." [http://edamontology.org]
synonym: "Cartesian y coordinate" EXACT [http://edamontology.org]
xref: WHATIF: PDBx_Cartn_y
is_a: EDAM_data:1743 ! Atomic coordinate
! _atom_site.Cartn_y in PDBML

[Term]
id: EDAM_data:1746
name: Atomic z coordinate
namespace: data
subset: data
def: "Cartesian z coordinate of an atom (in a molecular structure)." [http://edamontology.org]
synonym: "Cartesian z coordinate" EXACT [http://edamontology.org]
xref: WHATIF: PDBx_Cartn_z
is_a: EDAM_data:1743 ! Atomic coordinate
! _atom_site.Cartn_z in PDBML

[Term]
id: EDAM_data:0844
name: Molecular mass
namespace: data
subset: data
def: "Mass of a molecule." [http://edamontology.org]
is_a: EDAM_data:2050 ! Molecular property (general)

[Term]
id: EDAM_data:0845
name: Molecular charge
namespace: data
subset: data
def: "Net charge of a molecule." [http://edamontology.org]
is_a: EDAM_data:2050 ! Molecular property (general)
! pdbx_formal_charge in PDBML


[Term]
id: EDAM_data:0846
name: Chemical formula
namespace: data
subset: data
def: "A specification of a chemical structure." [http://edamontology.org]
synonym: "Chemical structure specification" EXACT [http://edamontology.org]
is_a: EDAM_data:2050 ! Molecular property (general)


[Term]
id: EDAM_data:0847
name: QSAR descriptor
namespace: data
subset: data
def: "A QSAR quantitative descriptor (name-value pair) of chemical structure." [http://edamontology.org]
comment: QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications.
is_a: EDAM_data:2050 ! Molecular property (general)

[Term]
id: EDAM_data:2301
name: SMILES string
namespace: data
subset: data
def: "A specification of a chemical structure in SMILES format." [http://edamontology.org]
is_a: EDAM_data:0846 ! Chemical formula

! Many subtypes of the individual descriptors below (not included here) cover all types of protein properties.

[Term]
id: EDAM_data:1201
name: QSAR descriptor (constitutional)
namespace: data
subset: data
def: "A QSAR constitutional descriptor." [http://edamontology.org]
synonym: "QSAR constitutional descriptor" EXACT [http://edamontology.org]
is_a: EDAM_data:0847 ! QSAR descriptor


[Term]
id: EDAM_data:1202
name: QSAR descriptor (electronic)
namespace: data
subset: data
def: "A QSAR electronic descriptor." [http://edamontology.org]
synonym: "QSAR electronic descriptor" EXACT [http://edamontology.org]
is_a: EDAM_data:0847 ! QSAR descriptor


[Term]
id: EDAM_data:1203
name: QSAR descriptor (geometrical)
namespace: data
subset: data
def: "A QSAR geometrical descriptor." [http://edamontology.org]
synonym: "QSAR geometrical descriptor" EXACT [http://edamontology.org]
is_a: EDAM_data:0847 ! QSAR descriptor


[Term]
id: EDAM_data:1204
name: QSAR descriptor (topological)
namespace: data
subset: data
def: "A QSAR topological descriptor." [http://edamontology.org]
synonym: "QSAR topological descriptor" EXACT [http://edamontology.org]
is_a: EDAM_data:0847 ! QSAR descriptor


[Term]
id: EDAM_data:1205
name: QSAR descriptor (molecular)
namespace: data
subset: data
def: "A QSAR molecular descriptor." [http://edamontology.org]
synonym: "QSAR molecular descriptor" EXACT [http://edamontology.org]
is_a: EDAM_data:0847 ! QSAR descriptor

[Term]
id: EDAM_data:0848
name: Raw sequence
namespace: data
subset: data
def: "A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters." [http://edamontology.org]
comment: Non-sequence characters may be used for example for gaps and translation stop.
is_a: EDAM_data:2044 ! Sequence


[Term]
id: EDAM_data:2201
name: Sequence record full
namespace: data
subset: data
def: "A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org]
xref: SO:2000061
is_a: EDAM_data:0849 ! Sequence record


[Term]
id: EDAM_data:2888
name: Sequence record full (protein)
namespace: data
subset: data
def: "A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org]
xref: SO:2000061
is_a: EDAM_data:2201 ! Sequence record full
is_a: EDAM_data:2886 ! Sequence record (protein)

[Term]
id: EDAM_data:2889
name: Sequence record full (nucleic acid)
namespace: data
subset: data
def: "A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org]
xref: SO:2000061
is_a: EDAM_data:2201 ! Sequence record full
is_a: EDAM_data:2887 ! Sequence record (nucleic acid)

[Term]
id: EDAM_data:0849
name: Sequence record
namespace: data
subset: data
! alt_id: EDAM_data:1220
! alt_id: EDAM_data:1224
! alt_id: EDAM_data:1225
! alt_id: EDAM_data:1226
! alt_id: EDAM_data:1227
! alt_id: EDAM_data:1229
! alt_id: EDAM_data:1230
! alt_id: EDAM_data:1231
! alt_id: EDAM_data:1232
def: "A molecular sequence and associated metadata." [http://edamontology.org]
is_a: EDAM_data:2044 ! Sequence


[Term]
id: EDAM_data:2886
name: Sequence record (protein)
namespace: data
subset: data
! alt_id: EDAM_data:1222
def: "A protein sequence and associated metadata." [http://edamontology.org]
synonym: "Protein sequence record" EXACT [http://edamontology.org]
is_a: EDAM_data:0849 ! Sequence record
is_a: EDAM_data:2976 ! Protein sequence

[Term]
id: EDAM_data:2887
name: Sequence record (nucleic acid)
namespace: data
subset: data
! alt_id: EDAM_data:1221
def: "A nucleic acid sequence and associated metadata." [http://edamontology.org]
synonym: "Nucleic acid sequence record" EXACT [http://edamontology.org]
synonym: "Nucleotide sequence record" EXACT [http://edamontology.org]
is_a: EDAM_data:0849 ! Sequence record
is_a: EDAM_data:2977 ! Nucleic acid sequence


[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:2974
name: Raw sequence (protein)
namespace: data
subset: data
def: "A raw protein sequence (string of characters)." [http://edamontology.org]
is_a: EDAM_data:0848 ! Raw sequence
is_a: EDAM_data:2976 ! Protein sequence

[Term]
id: EDAM_data:2975
name: Raw sequence (nucleic acid)
namespace: data
subset: data
def: "A raw nucleic acid sequence." [http://edamontology.org]
is_a: EDAM_data:0848 ! Raw sequence
is_a: EDAM_data:2977 ! Nucleic acid sequence


[Term]
id: EDAM_data:2046
name: Sequence record lite (nucleic acid)
namespace: data
subset: data
def: "A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org]
is_a: EDAM_data:2043 ! Sequence record lite
is_a: EDAM_data:2887 ! Sequence record (nucleic acid)

[Term]
id: EDAM_data:2047
name: Sequence record lite (protein)
namespace: data
subset: data
def: "A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org]
is_a: EDAM_data:2043 ! Sequence record lite
is_a: EDAM_data:2886 ! Sequence record (protein)

[Term]
id: EDAM_data:2043
name: Sequence record lite
namespace: data
subset: data
! alt_id: EDAM_data:1223
def: "A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment." [http://edamontology.org]
is_a: EDAM_data:0849 ! Sequence record


[Term]
id: EDAM_data:2173
name: Sequence set (stream)
namespace: data
subset: data
def: "A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing." [http://edamontology.org]
comment: This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[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_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:1236
name: Psiblast checkpoint file
namespace: data
subset: data
def: "A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration." [http://edamontology.org]
comment: A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1237
name: HMMER synthetic sequences set
namespace: data
subset: data
def: "Sequences generated by HMMER package in FASTA-style format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set


[Term]
id: EDAM_data:1238
name: Proteolytic digest
namespace: data
subset: data
def: "A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses." [http://edamontology.org]
is_a: EDAM_data:1233 ! Sequence set (protein)
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

[Term]
id: EDAM_data:1766
name: CATH domain sequences (ATOM)
namespace: data
subset: data
def: "FASTA sequence database for all CATH domains (based on PDB ATOM records)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set


[Term]
id: EDAM_data:1767
name: CATH domain sequences (COMBS)
namespace: data
subset: data
def: "FASTA sequence database for all CATH domains (based on COMBS sequence data)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[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: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_data:1240
name: PCR primers
namespace: data
subset: data
def: "Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set." [http://edamontology.org]
is_a: EDAM_data:1234 ! Sequence set (nucleic acid)

[Term]
id: EDAM_data:1241
name: vectorstrip cloning vector definition file
namespace: data
subset: data
def: "File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1242
name: Primer3 internal oligo mishybridizing library
namespace: data
subset: data
def: "A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set


[Term]
id: EDAM_data:1243
name: Primer3 mispriming library file
namespace: data
subset: data
def: "A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1244
name: primersearch primer pairs sequence record
namespace: data
subset: data
def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1245
name: Sequence cluster (protein)
namespace: data
subset: data
def: "A cluster of protein sequences." [http://edamontology.org]
comment: The sequences are typically related, for example a family of sequences.
synonym: "Protein sequence cluster" EXACT [http://edamontology.org]
is_a: EDAM_data:1233 ! Sequence set (protein)
is_a: EDAM_data:1235 ! Sequence cluster


[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_data:1764
name: CATH representative domain sequences (ATOM)
namespace: data
subset: data
def: "FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1235 ! Sequence cluster


[Term]
id: EDAM_data:1765
name: CATH representative domain sequences (COMBS)
namespace: data
subset: data
def: "FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1235 ! Sequence cluster


[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_data:1253
name: Sequence information report
namespace: data
subset: data
def: "Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2043 ! Sequence record lite
consider: EDAM_data:0855 ! Sequence metadata

[Term]
id: EDAM_data:1254
name: Sequence property
namespace: data
subset: data
def: "An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis." [http://edamontology.org]
synonym: "Sequence properties report" EXACT [http://edamontology.org]
is_a: EDAM_data:2955 ! Sequence report


[Term]
id: EDAM_data:1255
name: Feature record
namespace: data
subset: data
! alt_id: EDAM_data:1271
! alt_id: EDAM_data:1275
def: "Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence." [http://edamontology.org]
comment: This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features.  General feature reports are a source of sequence feature table information although internal conversion would be required.
synonym: "Sequence features" EXACT [http://edamontology.org]
synonym: "Sequence features report" EXACT [http://edamontology.org]
synonym: "General sequence features" EXACT [http://edamontology.org]
synonym: "sequence_feature" RELATED [SO:0000110]
is_a: EDAM_data:2955 ! Sequence report


[Term]
id: EDAM_data:2914
name: Sequence features metadata
namespace: data
subset: data
def: "Metadata on sequence features." [http://edamontology.org]
is_a: EDAM_data:0855 ! Sequence metadata


[Term]
id: EDAM_data:1020
name: Sequence feature key
namespace: data
subset: data
def: "The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key." [http://edamontology.org]
comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.
synonym: "Sequence feature type" EXACT [http://edamontology.org]
synonym: "Sequence feature method" EXACT [http://edamontology.org]
is_a: EDAM_data:2914 ! Sequence features metadata


[Term]
id: EDAM_data:1021
name: Sequence feature qualifier
namespace: data
subset: data
def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org]
comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location.
is_a: EDAM_data:2914 ! Sequence features metadata

[Term]
id: EDAM_data:1022
name: Sequence feature label
namespace: data
subset: data
def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org]
comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.
synonym: "Sequence feature name" EXACT [http://edamontology.org]
is_a: EDAM_data:2914 ! Sequence features metadata

[Term]
id: EDAM_data:1278
name: Genetic map
namespace: data
subset: data
def: "A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies." [http://edamontology.org]
comment: A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.
synonym: "Linkage map" EXACT [http://edamontology.org]
xref: Moby:GeneticMap
is_a: EDAM_data:1274 ! Map
relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage

[Term]
id: EDAM_data:1283
name: Cytogenetic map
namespace: data
subset: data
! alt_id: EDAM_data:1287
def: "A map showing banding patterns derived from direct observation of a stained chromosome." [http://edamontology.org]
comment: This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances.  Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.
synonym: "Cytologic map" EXACT [http://edamontology.org]
synonym: "Cytogenic map" EXACT [http://edamontology.org]
synonym: "Chromosome map" EXACT [http://edamontology.org]
is_a: EDAM_data:1280 ! Physical map


[Term]
id: EDAM_data:2870
name: Radiation hybrid map
namespace: data
subset: data
def: "A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome." [http://edamontology.org]
comment: The radiation method can break very closely linked markers providing a more detailed map.  Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.
synonym: "RH map" EXACT [http://edamontology.org]
is_a: EDAM_data:1280 ! Physical map

[Term]
id: EDAM_data:1279
name: Sequence map
namespace: data
subset: data
def: "A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs." [http://edamontology.org]
comment: A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.
is_a: EDAM_data:1280 ! Physical map

[Term]
id: EDAM_data:1280
name: Physical map
namespace: data
subset: data
def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [http://edamontology.org]
comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
is_a: EDAM_data:1274 ! Map


[Term]
id: EDAM_data:1284
name: DNA transduction map
namespace: data
subset: data
def: "A gene map showing distances between loci based on relative cotransduction frequencies." [http://edamontology.org]
is_a: EDAM_data:1278 ! Genetic map


[Term]
id: EDAM_data:1860
name: QTL map
namespace: data
subset: data
def: "A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers." [http://edamontology.org]
synonym: "Quantitative trait locus map" EXACT [http://edamontology.org]
is_a: EDAM_data:1278 ! Genetic map

[Term]
id: EDAM_data:1859
name: Deletion map
namespace: data
subset: data
def: "A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type." [http://edamontology.org]
comment: A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.
synonym: "Deletion-based cytogenetic map" EXACT [http://edamontology.org]
is_a: EDAM_data:1283 ! Cytogenetic map

[Term]
id: EDAM_data:1863
name: Haplotype map
namespace: data
subset: data
def: "A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation." [http://edamontology.org]
xref: Moby:Haplotyping_Study_obj
is_a: EDAM_data:1278 ! Genetic map


[Term]
id: EDAM_data:1285
name: Gene map
namespace: data
subset: data
def: "Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene." [http://edamontology.org]
is_a: EDAM_data:1279 ! Sequence map


[Term]
id: EDAM_data:1286
name: Plasmid map
namespace: data
subset: data
def: "Sequence map of a plasmid (circular DNA)." [http://edamontology.org]
is_a: EDAM_data:1279 ! Sequence map

[Term]
id: EDAM_data:1288
name: Genome map
namespace: data
subset: data
def: "Sequence map of a whole genome." [http://edamontology.org]
is_a: EDAM_data:1279 ! Sequence map


[Term]
id: EDAM_data:1865
name: Map feature
namespace: data
subset: data
def: "A feature which may mapped (positioned) on a genetic or other type of map." [http://edamontology.org]
comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
xref: Moby:MapFeature
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1255 ! Feature record
consider: EDAM_data:2019 ! Map attribute
consider: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:1257
name: Sequence property (protein)
namespace: data
subset: data
def: "A report of general sequence properties derived from protein sequence data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1258
name: Sequence property (nucleic acid)
namespace: data
subset: data
def: "A report of general sequence properties derived from nucleotide sequence data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0912 ! Nucleic acid property


[Term]
id: EDAM_data:1259
name: Sequence complexity
namespace: data
subset: data
def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [http://edamontology.org]
synonym: "Sequence property (complexity)" EXACT [http://edamontology.org]
is_a: EDAM_data:1254 ! Sequence property


[Term]
id: EDAM_data:1260
name: Sequence ambiguity
namespace: data
subset: data
def: "A report on ambiguity in molecular sequence(s)." [http://edamontology.org]
synonym: "Sequence property (ambiguity)" EXACT [http://edamontology.org]
is_a: EDAM_data:1254 ! Sequence property


[Term]
id: EDAM_data:1261
name: Sequence composition
namespace: data
subset: data
def: "A report (typically a table) on character or word composition / frequency of a molecular sequence(s)." [http://edamontology.org]
synonym: "Sequence property (composition)" EXACT [http://edamontology.org]
is_a: EDAM_data:1254 ! Sequence property


[Term]
id: EDAM_data:3119 {since=beta13}
name: Sequence features (compositionally-biased regions)
namespace: data
subset: data
def: "A report of regions in a molecular sequence that are biased to certain characters." [http://edamontology.org]
is_a: EDAM_data:1261 ! Sequence composition




[Term]
id: EDAM_data:3085 {since=beta13}
name: Protein sequence composition
namespace: data
subset: data
def: "A report (typically a table) on character or word composition / frequency of protein sequence(s)." [http://edamontology.org]
synonym: "Sequence property (protein composition)" EXACT [http://edamontology.org]
is_a: EDAM_data:1261 ! Sequence composition

[Term]
id: EDAM_data:3086 {since=beta13}
name: Nucleic acid sequence composition
namespace: data
subset: data
def: "A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s)." [http://edamontology.org]
synonym: "Sequence property (nucleic acid composition)" EXACT [http://edamontology.org]
is_a: EDAM_data:1261 ! Sequence composition
is_a: EDAM_data:0912 ! Nucleic acid property



[Term]
id: EDAM_data:1262
name: Peptide molecular weight hits
namespace: data
subset: data
def: "A report on peptide fragments of certain molecular weight(s) in one or more protein sequences." [http://edamontology.org]
is_a: EDAM_data:1233 ! Sequence set (protein)

[Term]
id: EDAM_data:1263
name: Sequence composition (base position variability)
namespace: data
subset: data
def: "Report on or plot of third base position variability in a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:3086 ! Nucleic acid sequence composition


[Term]
id: EDAM_data:2157
name: Word composition
namespace: data
subset: data
def: "Word composition data for a molecular sequence." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1268 ! Amino acid word frequencies
consider: EDAM_data:1266 ! Sequence composition (base words)

[Term]
id: EDAM_data:1264
name: Sequence composition table
namespace: data
subset: data
def: "A table of character or word composition / frequency of a molecular sequence." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1261 ! Sequence composition

[Term]
id: EDAM_data:2166
name: Sequence composition plot
namespace: data
subset: data
def: "A plot of character or word composition / frequency of a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:1261 ! Sequence composition

[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:1267
name: Amino acid frequencies
namespace: data
subset: data
def: "A table of amino acid frequencies of a protein sequence." [http://edamontology.org]
synonym: "Sequence composition (amino acid frequencies)" EXACT [http://edamontology.org]
is_a: EDAM_data:3085 ! Protein sequence composition


[Term]
id: EDAM_data:1266
name: Sequence composition (base words)
namespace: data
subset: data
def: "A table of word composition of a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:3086 ! Nucleic acid sequence composition


[Term]
id: EDAM_data:1268
name: Amino acid word frequencies
namespace: data
subset: data
def: "A table of amino acid word composition of a protein sequence." [http://edamontology.org]
synonym: "Sequence composition (amino acid words)" EXACT [http://edamontology.org]
is_a: EDAM_data:3085 ! Protein sequence composition



[Term]
id: EDAM_data:1269
name: DAS sequence feature annotation
namespace: data
subset: data
def: "Annotation of a molecular sequence in DAS format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1978 ! DASGFF


[Term]
id: EDAM_data:3002
name: Sequence annotation track
namespace: data
subset: data
def: "Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser." [http://edamontology.org]
synonym: "Annotation track" EXACT [http://edamontology.org]
synonym: "Genome track" EXACT [http://edamontology.org]
synonym: "Genomic track" EXACT [http://edamontology.org]
synonym: "Genome-browser track" EXACT [http://edamontology.org]
synonym: "Genome annotation track" EXACT [http://edamontology.org]
is_a: EDAM_data:1255 ! Feature record


[Term]
id: EDAM_data:1270
name: Sequence feature table
namespace: data
subset: data
def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org]
synonym: "Feature table" EXACT [http://edamontology.org]
is_a: EDAM_data:1255 ! Feature record


[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_data:3139 {since=beta13}
name: Nucleic acid features (STS)
namespace: data
subset: data
def: "A report on sequence tagged sites (STS) in nucleic acid sequences." [http://edamontology.org]
comment: Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.
is_a: EDAM_data:1276 ! Nucleic acid features


[Term]
id: EDAM_data:3122 {since=beta13}
name: Nucleic acid features (difference and change)
namespace: data
subset: data
def: "A report on features in a nucleic acid sequence that indicate changes to or differences between sequences." [http://edamontology.org]
is_a: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:3123 {since=beta13}
name: Nucleic acid features (expression signal)
namespace: data
subset: data
def: "A report on regions within a nucleic acid sequence containing a signal that alters a biological function." [http://edamontology.org]
is_a: EDAM_data:1276 ! Nucleic acid features


[Term]
id: EDAM_data:3125 {since=beta13}
name: Nucleic acid features (binding)
namespace: data
subset: data
def: "A report on regions of a nucleic acid sequence that bind some other molecule." [http://edamontology.org]
comment: This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).
is_a: EDAM_data:1276 ! Nucleic acid features


[Term]
id: EDAM_data:3126 {since=beta13}
name: Nucleic acid features (repeats)
namespace: data
subset: data
def: "A report on repetitive elements within a nucleic acid sequence." [http://edamontology.org]
comment: This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at  both ends of a defined sequence and other types of repeating unit.
is_a: EDAM_data:1299 ! Sequence features (repeats)
is_a: EDAM_data:1276 ! Nucleic acid features


[Term]
id: EDAM_data:3127 {since=beta13}
name: Nucleic acid features (replication and recombination)
namespace: data
subset: data
def: "A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination." [http://edamontology.org]
comment: This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.
is_a: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:3128 {since=beta13}
name: Nucleic acid features (structure)
namespace: data
subset: data
def: "A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:3132 {since=beta13}
name: Nucleic acid features (d-loop)
namespace: data
subset: data
def: "A report on displacement loops in a mitochondrial DNA sequence." [http://edamontology.org]
comment: A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
is_a: EDAM_data:3128 ! Nucleic acid features (structure)

[Term]
id: EDAM_data:3133 {since=beta13}
name: Nucleic acid features (stem loop)
namespace: data
subset: data
def: "A report on stem loops in a DNA sequence." [http://edamontology.org]
comment: A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.
is_a: EDAM_data:3128 ! Nucleic acid features (structure)


[Term]
id: EDAM_data:2882
name: DNA features
namespace: data
subset: data
def: "DNA sequence-specific feature annotation (not in a feature table)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:2883
name: Nucleic acid features (RNA features)
namespace: data
subset: data
def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org]
synonym: "RNA features" EXACT [http://edamontology.org]
is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)

[Term]
id: EDAM_data:3134 {since=beta13}
name: Nucleic acid features (mRNA features)
namespace: data
subset: data
def: "Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules." [http://edamontology.org]
comment: This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
synonym: "mRNA features" EXACT [http://edamontology.org]
is_a: EDAM_data:2883 ! Nucleic acid features (RNA features)


[Term]
id: EDAM_data:3137 {since=beta13}
name: Nucleic acid features (non-coding RNA)
namespace: data
subset: data
def: "Features concerning non-coding or functional RNA molecules, including tRNA and rRNA." [http://edamontology.org]
synonym: "ncRNA features" EXACT [http://edamontology.org]
synonym: "Non-coding RNA features" EXACT [http://edamontology.org]
is_a: EDAM_data:2883 ! Nucleic acid features (RNA features)

[Term]
id: EDAM_data:3138 {since=beta13}
name: Nucleic acid features (transcriptional)
namespace: data
subset: data
def: "Features concerning transcription of DNA into RNA including the regulation of transcription." [http://edamontology.org]
comment: This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
is_a: EDAM_data:2883 ! Nucleic acid features (RNA features)


[Term]
id: EDAM_data:1277
name: Protein features
namespace: data
subset: data
! alt_id: EDAM_data:1272
def: "Protein sequence-specific feature annotation (positional features of a protein sequence)." [http://edamontology.org]
comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.
synonym: "Feature table (protein)" EXACT [http://edamontology.org]
synonym: "Protein feature table" EXACT [http://edamontology.org]
is_a: EDAM_data:1255 ! Feature record
is_a: EDAM_data:0896 ! Protein report


[Term]
id: EDAM_data:1256
name: Sequence features (comparative)
namespace: data
subset: data
def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
is_obsolete: true !{since=beta13}
consider: EDAM_data:1255 ! Feature record


[Term]
id: EDAM_data:1298
name: Sequence features (motifs)
namespace: data
subset: data
def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org]
comment: Use this concept if another, more specific concept is not available.
is_a: EDAM_data:1255 ! Feature record

[Term]
id: EDAM_data:3130 {since=beta13}
name: Protein features (motifs)
namespace: data
subset: data
def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences." [http://edamontology.org]
comment: Use this concept if another, more specific concept is not available.
is_a: EDAM_data:1277 ! Protein features
is_a: EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_data:3131 {since=beta13}
name: Nucleic acid features (motifs)
namespace: data
subset: data
def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences." [http://edamontology.org]
comment: Use this concept if another, more specific concept is not available.
is_a: EDAM_data:1276 ! Nucleic acid features
is_a: EDAM_data:1298 ! Sequence features (motifs)


[Term]
id: EDAM_data:0858
name: Database hits (secondary)
namespace: data
subset: data
def: "A report of hits from a search of a protein secondary or domain database." [http://edamontology.org]
comment: Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'.
is_a: EDAM_data:2080 ! Database hits


[Term]
id: EDAM_data:0901
name: Protein features (domains)
namespace: data
subset: data
def: "Summary of structural domains or 3D folds in a protein or polypeptide chain." [http://edamontology.org]
comment: The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.
synonym: "Protein domain assignment" EXACT [http://edamontology.org]
synonym: "Protein structural domains" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
relationship: has_topic EDAM_topic:0736 ! Protein domains and folds

[Term]
id: EDAM_data:3118 {since=beta13}
name: Protein features (topological domains)
namespace: data
subset: data
def: "Summary of topological domains such as cytoplasmic regions in a protein." [http://edamontology.org]
synonym: "Protein topological domains" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
relationship: has_topic EDAM_topic:0736 ! Protein domains and folds






[Term]
id: EDAM_data:1299
name: Sequence features (repeats)
namespace: data
subset: data
! alt_id: EDAM_data:1282
def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org]
comment: The report might include derived data map such as classification, annotation, organization, periodicity etc.
synonym: "Repeat sequence map" EXACT [http://edamontology.org]
is_a: EDAM_data:1255 ! Feature record


[Term]
id: EDAM_data:3129 {since=beta13}
name: Protein features (repeats)
namespace: data
subset: data
def: "Location of short repetitive subsequences (repeat sequences) in a protein sequence." [http://edamontology.org]
is_a: EDAM_data:1299 ! Sequence features (repeats)
is_a: EDAM_data:1277 ! Protein features



[Term]
id: EDAM_data:1281
name: Sequence signature map
namespace: data
subset: data
def: "Image of a sequence with matches to signatures, motifs or profiles." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)


[Term]
id: EDAM_data:1290
name: InterPro compact match image
namespace: data
subset: data
def: "Image showing matches between protein sequence(s) and InterPro Entries." [http://edamontology.org]
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_data:1291
name: InterPro detailed match image
namespace: data
subset: data
def: "Image showing detailed information on matches between protein sequence(s) and InterPro Entries." [http://edamontology.org]
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_data:1292
name: InterPro architecture image
namespace: data
subset: data
def: "Image showing the architecture of InterPro domains in a protein sequence." [http://edamontology.org]
comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)

[Term]
id: EDAM_data:1293
name: SMART protein schematic
namespace: data
subset: data
def: "SMART protein schematic in PNG format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)


[Term]
id: EDAM_data:1294
name: GlobPlot domain image
namespace: data
subset: data
def: "Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1298 ! Sequence features (motifs)


[Term]
id: EDAM_data:1564
name: Protein fold recognition report
namespace: data
subset: data
def: "A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s)." [http://edamontology.org]
comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0901 ! Protein features (domains)

[Term]
id: EDAM_data:1300
name: Nucleic acid features (gene and transcript structure)
namespace: data
subset: data
def: "A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc." [http://edamontology.org]
synonym: "Gene annotation (structure)" EXACT [http://edamontology.org]
is_a: EDAM_data:0916 ! Gene annotation
is_a: EDAM_data:1276 ! Nucleic acid features

[Term]
id: EDAM_data:3140 {since=beta13}
name: Nucleic acid features (immunoglobulin gene structure)
namespace: data
subset: data
def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org]
is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)




[Term]
id: EDAM_data:1301
name: Nucleic acid features (mobile genetic elements)
namespace: data
subset: data
def: "A report on a region of a nucleic acid sequence containin mobile genetic elements." [http://edamontology.org]
comment: This includes transposons, Plasmids, Bacteriophage elements and Group II introns.
synonym: "Nucleic acid features (transposons)" EXACT [http://edamontology.org]
is_a: EDAM_data:1276 ! Nucleic acid features


[Term]
id: EDAM_data:1302
name: Nucleic acid features (PolyA signal or site)
namespace: data
subset: data
def: "A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript." [http://edamontology.org]
comment: A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.
synonym: "PolyA signal" EXACT [http://edamontology.org]
synonym: "PolyA site" EXACT [http://edamontology.org]
is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features)




[Term]
id: EDAM_data:3135 {since=beta13}
name: Nucleic acid features (signal or transit peptide)
namespace: data
subset: data
def: "A report on a coding sequence for a signal or transit peptide." [http://edamontology.org]
comment: A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features)







[Term]
id: EDAM_data:1303
name: Nucleic acid features (quadruplexes)
namespace: data
subset: data
def: "A report on quadruplex-forming motifs in a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:3128 ! Nucleic acid features (structure)

[Term]
id: EDAM_data:1304
name: Nucleic acid features (CpG island and isochore)
namespace: data
subset: data
def: "A report or plot of CpG rich regions (isochores) in a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional)

[Term]
id: EDAM_data:1305
name: Nucleic acid features (restriction sites)
namespace: data
subset: data
def: "Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org]
is_a: EDAM_data:3125 ! Nucleic acid features (binding)

[Term]
id: EDAM_data:1306
name: Nucleic acid features (nucleosome exclusion sequences)
namespace: data
subset: data
def: "A report on nucleosome formation potential or exclusion sequence(s)." [http://edamontology.org]
is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination)

[Term]
id: EDAM_data:1307
name: Nucleic acid features (splice sites)
namespace: data
subset: data
! alt_id: EDAM_data:0915
def: "A report on splice sites in a nucleotide sequence or alternative RNA splicing events." [http://edamontology.org]
synonym: "Nucleic acid report (RNA splice model)" EXACT [http://edamontology.org]
synonym: "Nucleic acid report (RNA splicing)" EXACT [http://edamontology.org]
is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features)


[Term]
id: EDAM_data:1308
name: Nucleic acid features (matrix/scaffold attachment sites)
namespace: data
subset: data
def: "A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence." [http://edamontology.org]
is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional)


[Term]
id: EDAM_data:1309
name: Gene features (exonic splicing enhancer)
namespace: data
subset: data
def: "A report on exonic splicing enhancers (ESE) in an exon." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2397 ! Nucleic acid features (exon)


[Term]
id: EDAM_data:1310
name: Nucleic acid features (microRNA)
namespace: data
subset: data
def: "A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc." [http://edamontology.org]
is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA)
relationship: has_topic EDAM_topic:3060 ! Regulatory RNA

[Term]
id: EDAM_data:2169
name: Nucleic acid features (siRNA)
namespace: data
subset: data
def: "A report on siRNA duplexes in mRNA." [http://edamontology.org]
is_a: EDAM_data:3137 ! Nucleic acid features (non-coding RNA)
relationship: has_topic EDAM_topic:3060 ! Regulatory RNA

[Term]
id: EDAM_data:0922
name: Nucleic acid features (primers)
namespace: data
subset: data
def: "Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence." [http://edamontology.org]
is_a: EDAM_data:3127 ! Nucleic acid features (replication and recombination)
relationship: has_topic EDAM_topic:0632 ! Probes and primers

[Term]
id: EDAM_data:1311
name: Nucleic acid features (operon)
namespace: data
subset: data
def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org]
comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.
synonym: "Gene features (operon)" EXACT [http://edamontology.org]
is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)

[Term]
id: EDAM_data:1312
name: Gene features (promoter)
namespace: data
subset: data
def: "A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence." [http://edamontology.org]
is_a: EDAM_data:3138 ! Nucleic acid features (transcriptional)


[Term]
id: EDAM_data:1313
name: Nucleic acid features (coding sequence)
namespace: data
subset: data
! alt_id: EDAM_data:1317
def: "A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames." [http://edamontology.org]
synonym: "Gene features (coding sequence)" EXACT [http://edamontology.org]
synonym: "Gene features (coding region)" EXACT [http://edamontology.org]
synonym: "Gene annotation (translation)" EXACT [http://edamontology.org]
is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features)

[Term]
id: EDAM_data:1314
name: Gene features (SECIS element)
namespace: data
subset: data
def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure)


[Term]
id: EDAM_data:1315
name: Gene features (TFBS)
namespace: data
subset: data
def: "A report on the transcription factor binding sites (TFBS) in a DNA sequence." [http://edamontology.org]
is_a: EDAM_data:1312 ! Gene features (promoter)
is_a: EDAM_data:3125 ! Nucleic acid features (binding)
relationship: has_topic EDAM_topic:0749 ! Transcription factors and regulatory sites

[Term]
id: EDAM_data:2397
name: Nucleic acid features (exon)
namespace: data
subset: data
def: "An informative report on an exon in a nucleotide sequences." [http://edamontology.org]
synonym: "Gene features (exon)" EXACT [http://edamontology.org]
is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence)

[Term]
id: EDAM_data:2754
name: Nucleic acid features (intron)
namespace: data
subset: data
def: "An informative report on an intron in a nucleotide sequences." [http://edamontology.org]
synonym: "Gene features (intron)" EXACT [http://edamontology.org]
is_a: EDAM_data:3134 ! Nucleic acid features (mRNA features)


[Term]
id: EDAM_data:2160
name: Fickett testcode plot
namespace: data
subset: data
def: "A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences." [http://edamontology.org]
is_a: EDAM_data:1313 ! Nucleic acid features (coding sequence)


[Term]
id: EDAM_data:1289
name: Restriction map
namespace: data
subset: data
def: "Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence." [http://edamontology.org]
is_a: EDAM_data:1305 ! Nucleic acid features (restriction sites)
is_a: EDAM_data:1279 ! Sequence map
is_a: EDAM_data:2969 ! Sequence image

[Term]
id: EDAM_data:1321
name: Protein features (sites)
namespace: data
subset: data
def: "A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites." [http://edamontology.org]
comment: Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1277 ! Protein features

[Term]
id: EDAM_data:1322
name: Protein features (signal peptides)
namespace: data
subset: data
def: "A report on the location of signal peptides or signal peptide cleavage sites in protein sequences." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features

[Term]
id: EDAM_data:3120 {since=beta13}
name: Protein features (sequence variants)
namespace: data
subset: data
def: "A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features



[Term]
id: EDAM_data:1323
name: Protein features (cleavage sites)
namespace: data
subset: data
def: "A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification


[Term]
id: EDAM_data:1324
name: Protein features (post-translation modifications)
namespace: data
subset: data
def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org]
synonym: "Protein features (post-translation modification sites)" EXACT [http://edamontology.org]
synonym: "Post-translation modification" EXACT [http://edamontology.org]
is_a: EDAM_data:2191 ! Protein features (chemical modification)

[Term]
id: EDAM_data:1325
name: Protein features (active sites)
namespace: data
subset: data
def: "A report on catalytic residues (active site) of an enzyme." [http://edamontology.org]
synonym: "Enzyme active site" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features

[Term]
id: EDAM_data:1326
name: Protein features (binding sites)
namespace: data
subset: data
def: "A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features


[Term]
id: EDAM_data:2989
name: Protein features (key folding sites)
namespace: data
subset: data
def: "A report on key residues involved in protein folding." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features



[Term]
id: EDAM_data:1327
name: Protein features (epitopes)
namespace: data
subset: data
def: "A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data." [http://edamontology.org]
comment: Epitope mapping is commonly done during vaccine design.
is_obsolete: true !{since=beta13}
consider: EDAM_data:1326 ! Protein features (binding sites)

[Term]
id: EDAM_data:1328
name: Protein features (nucleic acid binding sites)
namespace: data
subset: data
def: "A report on RNA and DNA-binding proteins and binding sites in protein sequences." [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features


[Term]
id: EDAM_data:1329
name: MHC Class I epitopes report
namespace: data
subset: data
def: "A report on epitopes that bind to MHC class I molecules." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1326 ! Protein features (binding sites)


[Term]
id: EDAM_data:1330
name: MHC Class II epitopes report
namespace: data
subset: data
def: "A report on predicted epitopes that bind to MHC class II molecules." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1326 ! Protein features (binding sites)

[Term]
id: EDAM_data:1331
name: Protein features (PEST sites)
namespace: data
subset: data
def: "A report or plot of PEST sites in a protein sequence." [http://edamontology.org]
comment: 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.
is_obsolete: true !{since=beta13}
consider: EDAM_data:1323 ! Protein features (cleavage sites)

[Term]
id: EDAM_data:0857
name: Database hits (sequence)
namespace: data
subset: data
def: "A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits." [http://edamontology.org]
comment: The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.
is_a: EDAM_data:2080 ! Database hits

[Term]
id: EDAM_data:0885
name: Database hits (structure)
namespace: data
subset: data
def: "Results (hits) from searching a database of tertiary structure." [http://edamontology.org]
comment: This includes alignment and score data.
is_a: EDAM_data:2080 ! Database hits


[Term]
id: EDAM_data:1338
name: Sequence database hits scores list
namespace: data
subset: data
def: "Scores from a sequence database search (for example a BLAST search)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0857 ! Database hits (sequence)


[Term]
id: EDAM_data:1339
name: Sequence database hits alignments list
namespace: data
subset: data
def: "Alignments from a sequence database search (for example a BLAST search)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0857 ! Database hits (sequence)

[Term]
id: EDAM_data:1340
name: Sequence database hits evaluation data
namespace: data
subset: data
def: "A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0857 ! Database hits (sequence)

[Term]
id: EDAM_data:1358
name: Prosite nucleotide pattern
namespace: data
subset: data
def: "A nucleotide regular expression pattern from the Prosite database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1353 ! Sequence motif


[Term]
id: EDAM_data:1359
name: Prosite protein pattern
namespace: data
subset: data
def: "A protein regular expression pattern from the Prosite database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_data:1352
name: Regular expression
namespace: data
subset: data
def: "Regular expression pattern." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter

[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:2071
name: Sequence motif (protein)
namespace: data
subset: data
def: "An amino acid sequence motif." [http://edamontology.org]
is_a: EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_data:2854
name: Position-specific scoring matrix
namespace: data
subset: data
def: "A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment." [http://edamontology.org]
is_a: EDAM_data:1354 ! Sequence profile
is_a: EDAM_data:2082 ! Matrix


[Term]
id: EDAM_data:1361
name: Position frequency matrix
namespace: data
subset: data
def: "A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org]
synonym: "PFM" EXACT [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix


[Term]
id: EDAM_data:1362
name: Position weight matrix
namespace: data
subset: data
def: "A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position." [http://edamontology.org]
comment: Contributions of individual sequences to the matrix might be uneven (weighted).
synonym: "PWM" EXACT [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix


[Term]
id: EDAM_data:1363
name: Information content matrix
namespace: data
subset: data
def: "A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position." [http://edamontology.org]
synonym: "ICM" EXACT [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix


[Term]
id: EDAM_data:1364
name: Hidden Markov model
namespace: data
subset: data
def: "A hidden Markov model representation of a set or alignment of sequences." [http://edamontology.org]
synonym: "HMM" EXACT [http://edamontology.org]
is_a: EDAM_data:1354 ! Sequence profile

[Term]
id: EDAM_data:1365
name: Fingerprint
namespace: data
subset: data
def: "One or more fingerprints (sequence classifiers) as used in the PRINTS database." [http://edamontology.org]
is_a: EDAM_data:2854 ! Position-specific scoring matrix


[Term]
id: EDAM_data:1368
name: Domainatrix signature
namespace: data
subset: data
def: "A protein signature of the type used in the EMBASSY Signature package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1354 ! Sequence profile

[Term]
id: EDAM_data:1371
name: HMMER NULL hidden Markov model
namespace: data
subset: data
def: "NULL hidden Markov model representation used by the HMMER package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1364 ! Hidden Markov model

[Term]
id: EDAM_data:1372
name: Protein family signature
namespace: data
subset: data
def: "A protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.
is_a: EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1373
name: Protein domain signature
namespace: data
subset: data
def: "A protein domain signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: Protein domain signatures identify structural or functional domains or other units with defined boundaries.
is_a: EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1374
name: Protein region signature
namespace: data
subset: data
def: "A protein region signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein region signature defines a region which cannot be described as a protein family or domain signature.
is_a: EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1375
name: Protein repeat signature
namespace: data
subset: data
def: "A protein repeat signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
is_a: EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1376
name: Protein site signature
namespace: data
subset: data
def: "A protein site signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein site signature is a classifier for a specific site in a protein.
is_a: EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1377
name: Protein conserved site signature
namespace: data
subset: data
def: "A protein conserved site signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.
is_a: EDAM_data:1376 ! Protein site signature

[Term]
id: EDAM_data:1378
name: Protein active site signature
namespace: data
subset: data
def: "A protein active site signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
is_a: EDAM_data:1376 ! Protein site signature

[Term]
id: EDAM_data:1379
name: Protein binding site signature
namespace: data
subset: data
def: "A protein binding site signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
is_a: EDAM_data:1376 ! Protein site signature

[Term]
id: EDAM_data:1380
name: Protein post-translational modification signature
namespace: data
subset: data
def: "A protein post-translational modification signature (sequence classifier) from the InterPro database." [http://edamontology.org]
comment: A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
is_a: EDAM_data:1376 ! Protein site signature

[Term]
id: EDAM_data:0861
name: Sequence alignment (words)
namespace: data
subset: data
def: "Alignment of exact matches between subsequences (words) within two or more molecular sequences." [http://edamontology.org]
synonym: "Sequence word alignment" EXACT [http://edamontology.org]
is_a: EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:0863
name: Sequence alignment
namespace: data
subset: data
def: "Alignment of multiple molecular sequences." [http://edamontology.org]
synonym: "Sequence alignment" EXACT [http://en.wikipedia.org/wiki/Sequence_alignment]
synonym: "sequence alignment" EXACT [http://semanticscience.org/resource/SIO_010066]
is_a: EDAM_data:1916 ! Alignment
relationship: has_topic EDAM_topic:0182 ! Sequence alignment

[Term]
id: EDAM_data:0868
name: Sequence profile alignment
namespace: data
subset: data
def: "A profile-profile alignment (each profile typically representing a sequence alignment)." [http://edamontology.org]
is_a: EDAM_data:1916 ! Alignment


[Term]
id: EDAM_data:0869
name: Sequence-profile alignment
namespace: data
subset: data
def: "Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment)." [http://edamontology.org]
comment: Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.
is_a: EDAM_data:1916 ! Alignment


[Term]
id: EDAM_data:2366
name: Secondary structure alignment
namespace: data
subset: data
def: "Alignment of the (1D representations of) secondary structure of two or more molecules." [http://edamontology.org]
is_a: EDAM_data:1916 ! Alignment


[Term]
id: EDAM_data:0878
name: Secondary structure alignment (protein)
namespace: data
subset: data
def: "Alignment of the (1D representations of) secondary structure of two or more proteins." [http://edamontology.org]
is_a: EDAM_data:2366 ! Secondary structure alignment
is_a: EDAM_data:3154 ! Protein alignment

[Term]
id: EDAM_data:0881
name: Secondary structure alignment (RNA)
namespace: data
subset: data
def: "Alignment of the (1D representations of) secondary structure of two or more RNA molecules." [http://edamontology.org]
xref: Moby:RNAStructAlignmentML
is_a: EDAM_data:2366 ! Secondary structure alignment


[Term]
id: EDAM_data:0886
name: Structure alignment
namespace: data
subset: data
def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org]
comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.
is_a: EDAM_data:1916 ! Alignment
is_a: EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0183 ! Structure alignment

[Term]
id: EDAM_data:0890
name: Structural (3D) profile alignment
namespace: data
subset: data
def: "A 3D profile-3D profile alignment (each profile representing structures or a structure alignment)." [http://edamontology.org]
synonym: "Structural profile alignment" EXACT [http://edamontology.org]
is_a: EDAM_data:1916 ! Alignment

[Term]
id: EDAM_data:0891
name: Sequence-3D profile alignment
namespace: data
subset: data
def: "An alignment of a sequence to a 3D profile (representing structures or a structure alignment)." [http://edamontology.org]
synonym: "Sequence-structural profile alignment" EXACT [http://edamontology.org]
is_a: EDAM_data:0893 ! Sequence-structure alignment

[Term]
id: EDAM_data:0893
name: Sequence-structure alignment
namespace: data
subset: data
def: "An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s))." [http://edamontology.org]
is_a: EDAM_data:1916 ! Alignment

[Term]
id: EDAM_data:1381
name: Sequence alignment (pair)
namespace: data
subset: data
def: "Alignment of exactly two molecular sequences." [http://edamontology.org]
synonym: "pairwise sequence alignment" RELATED [http://semanticscience.org/resource/SIO_010068] ! Related external synonym in EDAM without a note is usually almost exact.
is_a: EDAM_data:0863 ! Sequence alignment


[Term]
id: EDAM_data:1382
name: Sequence alignment (multiple)
namespace: data
subset: data
def: "Alignment of more than two molecular sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0863 ! Sequence alignment

[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_data:1384
name: Sequence alignment (protein)
namespace: data
subset: data
def: "Alignment of multiple protein sequences." [http://edamontology.org]
is_a: EDAM_data:0863 ! Sequence alignment
is_a: EDAM_data:3154 ! Protein alignment


[Term]
id: EDAM_data:1385
name: Sequence alignment (hybrid)
namespace: data
subset: data
def: "Alignment of multiple molecular sequences of different types." [http://edamontology.org]
comment: Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.
is_a: EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:1386
name: Sequence alignment (nucleic acid pair)
namespace: data
subset: data
def: "Alignment of exactly two nucleotide sequences." [http://edamontology.org]
is_a: EDAM_data:1381 ! Sequence alignment (pair)
is_a: EDAM_data:1383 ! Sequence alignment (nucleic acid)

[Term]
id: EDAM_data:1387
name: Sequence alignment (protein pair)
namespace: data
subset: data
def: "Alignment of exactly two protein sequences." [http://edamontology.org]
is_a: EDAM_data:1381 ! Sequence alignment (pair)
is_a: EDAM_data:1384 ! Sequence alignment (protein)


[Term]
id: EDAM_data:1389
name: Multiple nucleotide sequence alignment
namespace: data
subset: data
def: "Alignment of more than two nucleotide sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:1390
name: Multiple protein sequence alignment
namespace: data
subset: data
def: "Alignment of more than two protein sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:1388
name: Hybrid sequence alignment (pair)
namespace: data
subset: data
def: "Alignment of exactly two molecular sequences of different types." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1385 ! Sequence alignment (hybrid)


[Term]
id: EDAM_data:1417
name: Sequence-profile alignment (Domainatrix signature)
namespace: data
subset: data
def: "Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0869 ! Sequence-profile alignment


[Term]
id: EDAM_data:1418
name: Sequence-profile alignment (HMM)
namespace: data
subset: data
def: "Alignment of molecular sequence(s) to a hidden Markov model(s)." [http://edamontology.org]
is_a: EDAM_data:0869 ! Sequence-profile alignment

[Term]
id: EDAM_data:1420
name: Sequence-profile alignment (fingerprint)
namespace: data
subset: data
def: "Alignment of molecular sequences to a protein fingerprint from the PRINTS database." [http://edamontology.org]
is_a: EDAM_data:0869 ! Sequence-profile alignment


[Term]
id: EDAM_data:1479
name: Structure alignment (pair)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two molecular tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:0886 ! Structure alignment


[Term]
id: EDAM_data:1480
name: Structure alignment (multiple)
namespace: data
subset: data
def: "Alignment (superimposition) of more than two molecular tertiary (3D) structures." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0886 ! Structure alignment


[Term]
id: EDAM_data:1481
name: Structure alignment (protein)
namespace: data
subset: data
def: "Alignment (superimposition) of protein tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:0886 ! Structure alignment
is_a: EDAM_data:3154 ! Protein alignment

[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_data:1483
name: Structure alignment (protein pair)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:1481 ! Structure alignment (protein)
is_a: EDAM_data:1479 ! Structure alignment (pair)

[Term]
id: EDAM_data:1484
name: Multiple protein tertiary structure alignment
namespace: data
subset: data
def: "Alignment (superimposition) of more than two protein tertiary (3D) structures." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1481 ! Structure alignment (protein)

[Term]
id: EDAM_data:1485
name: Structure alignment (protein all atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org]
is_a: EDAM_data:1481 ! Structure alignment (protein)


[Term]
id: EDAM_data:1486
name: Structure alignment (protein C-alpha atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be considered.
is_a: EDAM_data:1481 ! Structure alignment (protein)


[Term]
id: EDAM_data:1487
name: Pairwise protein tertiary structure alignment (all atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1485 ! Structure alignment (protein all atoms)


[Term]
id: EDAM_data:1488
name: Pairwise protein tertiary structure alignment (C-alpha atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be included.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms)

[Term]
id: EDAM_data:1489
name: Multiple protein tertiary structure alignment (all atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1485 ! Structure alignment (protein all atoms)

[Term]
id: EDAM_data:1490
name: Multiple protein tertiary structure alignment (C-alpha atoms)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be included.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1486 ! Structure alignment (protein C-alpha atoms)

[Term]
id: EDAM_data:1491
name: Structure alignment (nucleic acid pair)
namespace: data
subset: data
def: "Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:1482 ! Structure alignment (nucleic acid)
is_a: EDAM_data:1479 ! Structure alignment (pair)

[Term]
id: EDAM_data:1492
name: Multiple nucleic acid tertiary structure alignment
namespace: data
subset: data
def: "Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1482 ! Structure alignment (nucleic acid)


[Term]
id: EDAM_data:1493
name: Structure alignment (RNA)
namespace: data
subset: data
def: "Alignment (superimposition) of RNA tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:1482 ! Structure alignment (nucleic acid)

[Term]
id: EDAM_data:0866
name: Sequence alignment metadata
namespace: data
subset: data
def: "Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score." [http://edamontology.org]
is_a: EDAM_data:0867 ! Sequence alignment report
is_a: EDAM_data:2337 ! Metadata


[Term]
id: EDAM_data:1414
name: Sequence alignment metadata (quality report)
namespace: data
subset: data
def: "Data on molecular sequence alignment quality (estimated accuracy)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0867 ! Sequence alignment report


[Term]
id: EDAM_data:1415
name: Sequence alignment report (site conservation)
namespace: data
subset: data
def: "Data on character conservation in a molecular sequence alignment." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
is_a: EDAM_data:0867 ! Sequence alignment report


[Term]
id: EDAM_data:1416
name: Sequence alignment report (site correlation)
namespace: data
subset: data
def: "Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures." [http://edamontology.org]
is_a: EDAM_data:0867 ! Sequence alignment report

[Term]
id: EDAM_data:2242
name: Phylogenetic property values
namespace: data
subset: data
def: "Phylogenetic property values data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0871 ! Phylogenetic character data


[Term]
id: EDAM_data:1444
name: Phylogenetic character contrasts
namespace: data
subset: data
def: "Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts." [http://edamontology.org]
synonym: "Phylogenetic report (character contrasts)" EXACT [http://edamontology.org]
is_a: EDAM_data:2523 ! Phylogenetic raw data

[Term]
id: EDAM_data:1426
name: Phylogenetic continuous quantitative data
namespace: data
subset: data
def: "Continuous quantitative data that may be read during phylogenetic tree calculation." [http://edamontology.org]
synonym: "Quantitative traits" EXACT [http://edamontology.org]
synonym: "Phylogenetic continuous quantitative characters" EXACT [http://edamontology.org]
is_a: EDAM_data:0871 ! Phylogenetic character data

[Term]
id: EDAM_data:2873
name: Phylogenetic gene frequencies data
namespace: data
subset: data
def: "Gene frequencies data that may be read during phylogenetic tree calculation." [http://edamontology.org]
is_a: EDAM_data:1426 ! Phylogenetic continuous quantitative data


[Term]
id: EDAM_data:1427
name: Phylogenetic discrete data
namespace: data
subset: data
def: "Character data with discrete states that may be read during phylogenetic tree calculation." [http://edamontology.org]
synonym: "Discretely coded characters" EXACT [http://edamontology.org]
synonym: "Discrete characters" EXACT [http://edamontology.org]
synonym: "Phylogenetic discrete states" EXACT [http://edamontology.org]
is_a: EDAM_data:0871 ! Phylogenetic character data

[Term]
id: EDAM_data:2994
name: Phylogenetic character weights
namespace: data
subset: data
def: "Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted." [http://edamontology.org]
is_a: EDAM_data:2523 ! Phylogenetic raw data

[Term]
id: EDAM_data:1428
name: Phylogenetic character cliques
namespace: data
subset: data
def: "One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny." [http://edamontology.org]
synonym: "Phylogenetic report (cliques)" EXACT [http://edamontology.org]
is_a: EDAM_data:2523 ! Phylogenetic raw data

[Term]
id: EDAM_data:1429
name: Phylogenetic invariants
namespace: data
subset: data
def: "Phylogenetic invariants data for testing alternative tree topologies." [http://edamontology.org]
synonym: "Phylogenetic report (invariants)" EXACT [http://edamontology.org]
is_a: EDAM_data:2523 ! Phylogenetic raw data


[Term]
id: EDAM_data:2247
name: Phylogenetic consensus tree
namespace: data
subset: data
def: "A consensus phylogenetic tree derived from comparison of multiple trees." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0872 ! Phylogenetic tree

[Term]
id: EDAM_data:1439
name: DNA substitution model
namespace: data
subset: data
def: "A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis." [http://edamontology.org]
synonym: "Sequence alignment report (DNA substitution model)" EXACT [http://edamontology.org]
synonym: "Phylogenetic tree report (DNA substitution model)" EXACT [http://edamontology.org]
is_a: EDAM_data:1438 ! Phylogenetic tree report
is_a: EDAM_data:0950 ! Biological model
is_a: EDAM_data:0867 ! Sequence alignment report


[Term]
id: EDAM_data:1440
name: Phylogenetic tree report (tree shape)
namespace: data
subset: data
def: "Data about the shape of a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_data:1438 ! Phylogenetic tree report

[Term]
id: EDAM_data:1441
name: Phylogenetic tree report (tree evaluation)
namespace: data
subset: data
def: "Data on the confidence of a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_data:1438 ! Phylogenetic tree report


[Term]
id: EDAM_data:1442
name: Phylogenetic tree report (tree distances)
namespace: data
subset: data
def: "Distances, such as Branch Score distance, between two or more phylogenetic trees." [http://edamontology.org]
is_a: EDAM_data:1438 ! Phylogenetic tree report

[Term]
id: EDAM_data:1443
name: Phylogenetic tree report (tree stratigraphic)
namespace: data
subset: data
def: "Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis." [http://edamontology.org]
is_a: EDAM_data:1438 ! Phylogenetic tree report

[Term]
id: EDAM_data:1446
name: Comparison matrix (integers)
namespace: data
subset: data
def: "Matrix of integer numbers for sequence comparison." [http://edamontology.org]
synonym: "Substitution matrix (integers)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0874 ! Comparison matrix

[Term]
id: EDAM_data:1447
name: Comparison matrix (floats)
namespace: data
subset: data
def: "Matrix of floating point numbers for sequence comparison." [http://edamontology.org]
synonym: "Substitution matrix (floats)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0874 ! Comparison matrix

[Term]
id: EDAM_data:1448
name: Comparison matrix (nucleotide)
namespace: data
subset: data
def: "Matrix of integer or floating point numbers for nucleotide comparison." [http://edamontology.org]
synonym: "Nucleotide substitution matrix" EXACT [http://edamontology.org]
is_a: EDAM_data:0874 ! Comparison matrix

[Term]
id: EDAM_data:1449
name: Comparison matrix (amino acid)
namespace: data
subset: data
def: "Matrix of integer or floating point numbers for amino acid comparison." [http://edamontology.org]
synonym: "Amino acid substitution matrix" EXACT [http://edamontology.org]
is_a: EDAM_data:2016 ! Amino acid property
is_a: EDAM_data:0874 ! Comparison matrix

[Term]
id: EDAM_data:1450
name: Nucleotide comparison matrix (integers)
namespace: data
subset: data
def: "Matrix of integer numbers for nucleotide comparison." [http://edamontology.org]
synonym: "Nucleotide substitution matrix (integers)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1448 ! Comparison matrix (nucleotide)


[Term]
id: EDAM_data:1451
name: Nucleotide comparison matrix (floats)
namespace: data
subset: data
def: "Matrix of floating point numbers for nucleotide comparison." [http://edamontology.org]
synonym: "Nucleotide substitution matrix (floats)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1448 ! Comparison matrix (nucleotide)


[Term]
id: EDAM_data:1452
name: Amino acid comparison matrix (integers)
namespace: data
subset: data
def: "Matrix of integer numbers for amino acid comparison." [http://edamontology.org]
synonym: "Amino acid substitution matrix (integers)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1449 ! Comparison matrix (amino acid)


[Term]
id: EDAM_data:1453
name: Amino acid comparison matrix (floats)
namespace: data
subset: data
def: "Matrix of floating point numbers for amino acid comparison." [http://edamontology.org]
synonym: "Amino acid substitution matrix (floats)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1449 ! Comparison matrix (amino acid)


[Term]
id: EDAM_data:1540
name: Protein residue interactions
namespace: data
subset: data
def: "Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups." [http://edamontology.org]
synonym: "Residue interaction data" EXACT [http://edamontology.org]
synonym: "Atom interaction data" EXACT [http://edamontology.org]
is_a: EDAM_data:2599 ! Molecular interaction
is_a: EDAM_data:0906 ! Protein interaction
relationship: has_topic EDAM_topic:0144 ! Protein residue interaction analysis

[Term]
id: EDAM_data:1543
name: Protein surface report
namespace: data
subset: data
def: "Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Protein structure report (surface)" EXACT [http://edamontology.org]
is_a: EDAM_data:1542 ! Protein solvent accessibility
is_a: EDAM_data:1537 ! Protein structure report


[Term]
id: EDAM_data:0875
name: Protein topology
namespace: data
subset: data
def: "Predicted or actual protein topology represented as a string of protein secondary structure elements." [http://edamontology.org]
comment: The location and size of the secondary structure elements and intervening loop regions is usually indicated.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0876 ! Protein features (secondary structure)

[Term]
id: EDAM_data:2081
name: Secondary structure
namespace: data
subset: data
def: "The secondary structure assignment (predicted or real) of a nucleic acid or protein." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:0877
name: Protein features (super-secondary)
namespace: data
subset: data
def: "A report of predicted or actual super-secondary structure of protein sequence(s)." [http://edamontology.org]
comment: Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
synonym: "Protein structure report (super-secondary)" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
is_a: EDAM_data:1537 ! Protein structure report

[Term]
id: EDAM_data:0902
name: Protein architecture report
namespace: data
subset: data
def: "An informative report on architecture (spatial arrangement of secondary structure) of a protein structure." [http://edamontology.org]
synonym: "Protein structure report (architecture)" EXACT [http://edamontology.org]
synonym: "Protein property (architecture)" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property
is_a: EDAM_data:1537 ! Protein structure report

[Term]
id: EDAM_data:0883
name: Structure
namespace: data
subset: data
def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org]
synonym: "Structure data" EXACT [http://edamontology.org]
comment: The coordinate data may be predicted or real.
relationship: has_topic EDAM_topic:0081 ! Structure analysis
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:0884
name: Tertiary structure record
namespace: data
subset: data
def: "An entry from a molecular tertiary (3D) structure database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0883 ! Structure


[Term]
id: EDAM_data:1546
name: Protein distance matrix
namespace: data
subset: data
def: "A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure." [http://edamontology.org]
is_a: EDAM_data:1540 ! Protein residue interactions


[Term]
id: EDAM_data:1547
name: Protein contact map
namespace: data
subset: data
def: "An amino acid residue contact map for a protein structure." [http://edamontology.org]
is_a: EDAM_data:1540 ! Protein residue interactions

[Term]
id: EDAM_data:1548
name: Protein residue 3D cluster
namespace: data
subset: data
def: "Report on clusters of contacting residues in protein structures such as a key structural residue network." [http://edamontology.org]
is_a: EDAM_data:1540 ! Protein residue interactions

[Term]
id: EDAM_data:1549
name: Protein hydrogen bonds
namespace: data
subset: data
def: "Patterns of hydrogen bonding in protein structures." [http://edamontology.org]
is_a: EDAM_data:1540 ! Protein residue interactions

[Term]
id: EDAM_data:1550
name: Protein non-canonical interactions
namespace: data
subset: data
def: "Non-canonical atomic interactions in protein structures." [http://edamontology.org]
synonym: "Protein non-canonical interactions report" EXACT [http://edamontology.org]
is_a: EDAM_data:1540 ! Protein residue interactions
is_a: EDAM_data:1539 ! Protein structural quality report

[Term]
id: EDAM_data:1542
name: Protein solvent accessibility
namespace: data
subset: data
def: "Data on the solvent accessible or buried surface area of a protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.
is_a: EDAM_data:1540 ! Protein residue interactions

[Term]
id: EDAM_data:0876
name: Protein features (secondary structure)
namespace: data
subset: data
def: "Secondary structure assignment (predicted or real) of a protein." [http://edamontology.org]
comment: The location and size of the secondary structure elements and intervening loop regions is typically given.  The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).
synonym: "Protein secondary structure" EXACT [http://edamontology.org]
is_a: EDAM_data:2081 ! Secondary structure
is_a: EDAM_data:1277 ! Protein features
relationship: has_topic EDAM_topic:0694 ! Protein secondary structure


[Term]
id: EDAM_data:0880
name: RNA secondary structure record
namespace: data
subset: data
def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org]
comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.
xref: Moby:RNAStructML
is_a: EDAM_data:2081 ! Secondary structure
relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment


[Term]
id: EDAM_data:1456
name: Protein features (membrane regions)
namespace: data
subset: data
def: "An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements." [http://edamontology.org]
comment: This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.
synonym: "Transmembrane region report" EXACT [http://edamontology.org]
synonym: "Intramembrane region report" EXACT [http://edamontology.org]
synonym: "Protein report (membrane protein)" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features

[Term]
id: EDAM_data:1755
name: Protein atom
namespace: data
subset: data
def: "Data on a single atom from a protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Atom data" EXACT [http://edamontology.org]
synonym: "atom" RELATED [CHEBI:33250]
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:1756
name: Protein residue
namespace: data
subset: data
def: "Data on a single amino acid residue position in a protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Residue" EXACT [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure

[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_data:1460
name: Protein structure
namespace: data
subset: data
def: "3D coordinate and associated data for a protein tertiary (3D) structure." [http://edamontology.org]
is_a: EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:2814 ! Protein structure analysis
relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure


[Term]
id: EDAM_data:1461
name: Protein-ligand complex
namespace: data
subset: data
def: "The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule." [http://edamontology.org]
comment: This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides.  For stable inter-polypeptide interactions use 'Protein complex' instead.
is_a: EDAM_data:1460 ! Protein structure


[Term]
id: EDAM_data:1462
name: Carbohydrate structure
namespace: data
subset: data
def: "3D coordinate and associated data for a carbohydrate (3D) structure." [http://edamontology.org]
is_a: EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0152 ! Carbohydrates
relationship: has_topic EDAM_topic:0153 ! Lipids

[Term]
id: EDAM_data:2850
name: Lipid structure
namespace: data
subset: data
def: "3D coordinate and associated data for a lipid structure." [http://edamontology.org]
is_a: EDAM_data:0883 ! Structure

[Term]
id: EDAM_data:1463
name: Small molecule structure
namespace: data
subset: data
def: "3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound." [http://edamontology.org]
synonym: "molecular entity" RELATED [CHEBI:23367]
is_a: EDAM_data:0883 ! Structure
relationship: has_topic EDAM_topic:0154 ! Small molecules

[Term]
id: EDAM_data:2851
name: Drug structure
namespace: data
subset: data
def: "3D coordinate and associated data for the (3D) structure of a drug." [http://edamontology.org]
is_a: EDAM_data:1463 ! Small molecule structure

[Term]
id: EDAM_data:2852
name: Toxin structure
namespace: data
subset: data
def: "3D coordinate and associated data for the (3D) structure of a toxin." [http://edamontology.org]
is_a: EDAM_data:1463 ! Small molecule structure


[Term]
id: EDAM_data:1464
name: DNA structure
namespace: data
subset: data
def: "3D coordinate and associated data for a DNA tertiary (3D) structure." [http://edamontology.org]
is_a: EDAM_data:1459 ! Nucleic acid structure

[Term]
id: EDAM_data:1465
name: RNA structure record
namespace: data
subset: data
def: "3D coordinate and associated data for an RNA tertiary (3D) structure." [http://edamontology.org]
is_a: EDAM_data:1459 ! Nucleic acid structure
relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment


[Term]
id: EDAM_data:1466
name: tRNA structure record
namespace: data
subset: data
def: "3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc." [http://edamontology.org]
is_a: EDAM_data:1465 ! RNA structure record

[Term]
id: EDAM_data:1467
name: Protein chain
namespace: data
subset: data
def: "3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain." [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:1468
name: Protein domain
namespace: data
subset: data
def: "3D coordinate and associated data for the tertiary (3D) structure of a protein domain." [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure
relationship: has_topic EDAM_topic:0736 ! Protein domains and folds

[Term]
id: EDAM_data:2877
name: Protein complex
namespace: data
subset: data
def: "3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another." [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:2878
name: Protein structural motif
namespace: data
subset: data
def: "3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role." [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:1469
name: Protein structure (all atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a protein tertiary (3D) structure (all atoms)." [http://edamontology.org]
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:1470
name: Protein structure (C-alpha atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be included.
is_a: EDAM_data:1460 ! Protein structure

[Term]
id: EDAM_data:1471
name: Protein chain (all atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1467 ! Protein chain
consider: EDAM_data:1469 ! Protein structure (all atoms)

[Term]
id: EDAM_data:1472
name: Protein chain (C-alpha atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be included.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1467 ! Protein chain
consider: EDAM_data:1470 ! Protein structure (C-alpha atoms)

[Term]
id: EDAM_data:1473
name: Protein domain (all atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1468 ! Protein domain
consider: EDAM_data:1469 ! Protein structure (all atoms)

[Term]
id: EDAM_data:1474
name: Protein domain (C-alpha atoms)
namespace: data
subset: data
def: "3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only)." [http://edamontology.org]
comment: C-beta atoms from amino acid side-chains may be included.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1468 ! Protein domain
consider: EDAM_data:1470 ! Protein structure (C-alpha atoms)


[Term]
id: EDAM_data:1495
name: DaliLite hit table
namespace: data
subset: data
def: "DaliLite hit table of protein chain tertiary structure alignment data." [http://edamontology.org]
comment: The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0887 ! Structure alignment report


[Term]
id: EDAM_data:1499
name: 3D-1D scoring matrix
namespace: data
subset: data
def: "A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments." [http://edamontology.org]
is_a: EDAM_data:0892 ! Protein sequence-structure scoring matrix


[Term]
id: EDAM_data:0894
name: Amino acid annotation
namespace: data
subset: data
def: "An informative report about a specific amino acid." [http://edamontology.org]
is_a: EDAM_data:2016 ! Amino acid property
is_a: EDAM_data:0962 ! Small molecule annotation



[Term]
id: EDAM_data:1501
name: Amino acid index
namespace: data
subset: data
def: "A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids." [http://edamontology.org]
is_a: EDAM_data:2016 ! Amino acid property
is_a: EDAM_data:2082 ! Matrix

[Term]
id: EDAM_data:1503
name: Amino acid pair-wise contact potentials
namespace: data
subset: data
def: "Statistical protein contact potentials." [http://edamontology.org]
is_a: EDAM_data:2016 ! Amino acid property

[Term]
id: EDAM_data:1502
name: Amino acid index (chemical classes)
namespace: data
subset: data
def: "Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids." [http://edamontology.org]
is_a: EDAM_data:1501 ! Amino acid index


[Term]
id: EDAM_data:1505
name: Amino acid index (molecular weight)
namespace: data
subset: data
def: "Molecular weights of amino acids." [http://edamontology.org]
is_a: EDAM_data:1501 ! Amino acid index

[Term]
id: EDAM_data:1506
name: Amino acid index (hydropathy)
namespace: data
subset: data
def: "Hydrophobic, hydrophilic or charge properties of amino acids." [http://edamontology.org]
is_a: EDAM_data:1501 ! Amino acid index


[Term]
id: EDAM_data:1507
name: Amino acid index (White-Wimley data)
namespace: data
subset: data
def: "Experimental free energy values for the water-interface and water-octanol transitions for the amino acids." [http://edamontology.org]
is_a: EDAM_data:1501 ! Amino acid index

[Term]
id: EDAM_data:1508
name: Amino acid index (van der Waals radii)
namespace: data
subset: data
def: "Van der Waals radii of atoms for different amino acid residues." [http://edamontology.org]
is_a: EDAM_data:1501 ! Amino acid index

[Term]
id: EDAM_data:1509
name: Enzyme property
namespace: data
subset: data
def: "An informative report on a specific enzyme." [http://edamontology.org]
synonym: "Enzyme report" EXACT [http://edamontology.org]
synonym: "Protein report (enzyme)" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property
relationship: has_topic EDAM_topic:0821 ! Enzymes and reactions

[Term]
id: EDAM_data:1776
name: Protein report (function)
namespace: data
subset: data
def: "Report on general functional properties of specific protein(s)." [http://edamontology.org]
comment: For properties that can be mapped to a sequence, use 'Sequence report' instead.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0896 ! Protein report



[Term]
id: EDAM_data:2722
name: Protein features (disordered structure)
namespace: data
subset: data
def: "An informative report about disordered structure in a protein." [http://edamontology.org]
synonym: "Protein structure report (disordered structure)" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
is_a: EDAM_data:1537 ! Protein structure report


[Term]
id: EDAM_data:2147
name: Protein report (transcription factor)
namespace: data
subset: data
def: "An informative report on a transcription factor protein." [http://edamontology.org]
comment: This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
synonym: "Transcription factor binding site data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0896 ! Protein report


[Term]
id: EDAM_data:2401
name: Protein report (membrane protein)
namespace: data
subset: data
def: "An informative report on a membrane protein." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1456 ! Protein features (membrane regions)


[Term]
id: EDAM_data:1517
name: Restriction enzyme property
namespace: data
subset: data
! alt_id: EDAM_data:1510
! alt_id: EDAM_data:1518
def: "An informative report on a specific restriction enzyme such as enzyme reference data." [http://edamontology.org]
comment:  This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
synonym: "Restriction enzyme report" EXACT [http://edamontology.org]
synonym: "Restriction enzyme pattern data" EXACT [http://edamontology.org]
synonym: "Protein report (restriction enzyme)" EXACT [http://edamontology.org]
is_a: EDAM_data:1509 ! Enzyme property


[Term]
id: EDAM_data:1533
name: Protein subcellular localization
namespace: data
subset: data
def: "An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins)." [http://edamontology.org]
synonym: "Protein report (subcellular localization)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0896 ! Protein report

[Term]
id: EDAM_data:2191
name: Protein features (chemical modification)
namespace: data
subset: data
def: "Data on a chemical modification of a protein." [http://edamontology.org]
synonym: "Protein modification annotation" EXACT [http://edamontology.org]
synonym: "protein modification" RELATED [MOD:00000]
synonym: "protein modification process" RELATED [GO:0006464]
is_a: EDAM_data:1277 ! Protein features


[Term]
id: EDAM_data:2991
name: Protein torsion angle data
namespace: data
subset: data
def: "Torsion angle data for a protein structure." [http://edamontology.org]
synonym: "Torsion angle data" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1544
name: Ramachandran plot
namespace: data
subset: data
def: "Phi/psi angle data or a Ramachandran plot of a protein structure." [http://edamontology.org]
is_a: EDAM_data:2991 ! Protein torsion angle data

[Term]
id: EDAM_data:1545
name: Protein dipole moment
namespace: data
subset: data
def: "Data on the net charge distribution (dipole moment) of a protein structure." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1519
name: Peptide molecular weights
namespace: data
subset: data
! alt_id: EDAM_data:1535
def: "List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents." [http://edamontology.org]
comment: The report might include associated data such as frequency of peptide fragment molecular weights.
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1520
name: Peptide hydrophobic moment
namespace: data
subset: data
def: "Report on the hydrophobic moment of a polypeptide sequence." [http://edamontology.org]
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
is_a: EDAM_data:2970 ! Protein hydropathy data

[Term]
id: EDAM_data:2970
name: Protein hydropathy data
namespace: data
subset: data
def: "A report on protein properties concerning hydropathy." [http://edamontology.org]
synonym: "Protein hydropathy report" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1521
name: Protein aliphatic index
namespace: data
subset: data
def: "The aliphatic index of a protein." [http://edamontology.org]
comment: The aliphatic index is the relative protein volume occupied by aliphatic side chains.
is_a: EDAM_data:2970 ! Protein hydropathy data


[Term]
id: EDAM_data:2164
name: Protein sequence properties plot
namespace: data
subset: data
def: "A plot of general physicochemical properties of a protein sequence." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:2165
name: Protein ionization curve
namespace: data
subset: data
def: "A plot of pK versus pH for a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1522
name: Protein sequence hydropathy plot
namespace: data
subset: data
def: "A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc." [http://edamontology.org]
comment: Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
is_a: EDAM_data:2970 ! Protein hydropathy data

[Term]
id: EDAM_data:1523
name: Protein charge plot
namespace: data
subset: data
def: "A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1524
name: Protein solubility
namespace: data
subset: data
def: "The solubility or atomic solvation energy of a protein sequence or structure." [http://edamontology.org]
synonym: "Protein solubility data" EXACT [http://edamontology.org]
is_a: EDAM_data:2970 ! Protein hydropathy data

[Term]
id: EDAM_data:1525
name: Protein crystallizability
namespace: data
subset: data
def: "Data on the crystallizability of a protein sequence." [http://edamontology.org]
synonym: "Protein crystallizability data" EXACT [http://edamontology.org]
is_a: EDAM_data:2970 ! Protein hydropathy data

[Term]
id: EDAM_data:1526
name: Protein globularity
namespace: data
subset: data
def: "Data on the stability, intrinsic disorder or globularity of a protein sequence." [http://edamontology.org]
synonym: "Protein globularity data" EXACT [http://edamontology.org]
is_a: EDAM_data:2970 ! Protein hydropathy data

[Term]
id: EDAM_data:1527
name: Protein titration curve
namespace: data
subset: data
def: "The titration curve of a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1528
name: Protein isoelectric point
namespace: data
subset: data
def: "The isoelectric point of one proteins." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1529
name: Protein pKa value
namespace: data
subset: data
def: "The pKa value of a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1530
name: Protein hydrogen exchange rate
namespace: data
subset: data
def: "The hydrogen exchange rate of a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1531
name: Protein extinction coefficient
namespace: data
subset: data
def: "The extinction coefficient of a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1532
name: Protein optical density
namespace: data
subset: data
def: "The optical density of a protein." [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property

[Term]
id: EDAM_data:1534
name: Peptide immunogenicity data
namespace: data
subset: data
def: "An report on allergenicity / immunogenicity of peptides and proteins." [http://edamontology.org]
comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
synonym: "Peptide immunogenicity report" EXACT [http://edamontology.org]
synonym: "Peptide immunogenicity" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:2957
name: Hopp and Woods plot
namespace: data
subset: data
def: "A Hopp and Woods plot of predicted antigenicity of a peptide or protein." [http://edamontology.org]
is_a: EDAM_data:1534 ! Peptide immunogenicity data

[Term]
id: EDAM_data:1536
name: MHC peptide immunogenicity report
namespace: data
subset: data
def: "A report on the immunogenicity of MHC class I or class II binding peptides." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1534 ! Peptide immunogenicity data


[Term]
id: EDAM_data:2753
name: Carbohydrate conformational map
namespace: data
subset: data
def: "A conformational energy map of the glycosidic linkages in a carbohydrate molecule." [http://edamontology.org]
is_a: EDAM_data:2313 ! Carbohydrate structure report

[Term]
id: EDAM_data:0899
name: Protein features (3D motif)
namespace: data
subset: data
def: "An informative report on the 3D structural motifs in a protein." [http://edamontology.org]
comment: This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc.
synonym: "Protein structure report (3D motif)" EXACT [http://edamontology.org]
is_a: EDAM_data:1277 ! Protein features
is_a: EDAM_data:1537 ! Protein structure report
relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces


[Term]
id: EDAM_data:1539
name: Protein structural quality report
namespace: data
subset: data
def: "Report on the quality of a protein three-dimensional model." [http://edamontology.org]
comment: Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.
synonym: "Protein structure report (quality evaluation)" EXACT [http://edamontology.org]
synonym: "Protein report (structural quality)" EXACT [http://edamontology.org]
synonym: "Protein property (structural quality)" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property
is_a: EDAM_data:1537 ! Protein structure report

[Term]
id: EDAM_data:1541
name: Protein flexibility or motion report
namespace: data
subset: data
def: "Informative report on flexibility or motion of a protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Protein structure report (flexibility or motion)" EXACT [http://edamontology.org]
synonym: "Protein property (flexibility or motion)" EXACT [http://edamontology.org]
synonym: "Protein flexibility or motion" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property
is_a: EDAM_data:1537 ! Protein structure report

[Term]
id: EDAM_data:2235
name: Raw SCOP domain classification
namespace: data
subset: data
def: "Raw SCOP domain classification data files." [http://edamontology.org]
comment: These are the parsable data files provided by SCOP.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_data:2236
name: Raw CATH domain classification
namespace: data
subset: data
def: "Raw CATH domain classification data files." [http://edamontology.org]
comment: These are the parsable data files provided by CATH.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_data:1762
name: CATH domain report
namespace: data
subset: data
def: "Summary of domain classification information for a CATH domain." [http://edamontology.org]
comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_data:1553
name: CATH node
namespace: data
subset: data
def: "Information on a node from the CATH database." [http://edamontology.org]
comment: The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.
synonym: "CATH classification node report" EXACT [http://edamontology.org]
is_a: EDAM_data:3101 ! Protein domain classification node


[Term]
id: EDAM_data:1554
name: SCOP node
namespace: data
subset: data
def: "Information on a node from the SCOP database." [http://edamontology.org]
synonym: "SCOP classification node" EXACT [http://edamontology.org]
is_a: EDAM_data:3101 ! Protein domain classification node


[Term]
id: EDAM_data:3141 {since=beta13}
name: SCOP class
namespace: data
subset: data
def: "Information on a 'class' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:3142 {since=beta13}
name: SCOP fold
namespace: data
subset: data
def: "Information on a 'fold' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:3143 {since=beta13}
name: SCOP superfamily
namespace: data
subset: data
def: "Information on a 'superfamily' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:3144 {since=beta13}
name: SCOP family
namespace: data
subset: data
def: "Information on a 'family' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:3145 {since=beta13}
name: SCOP protein
namespace: data
subset: data
def: "Information on a 'protein' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:3146 {since=beta13}
name: SCOP species
namespace: data
subset: data
def: "Information on a 'species' node from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1554 ! SCOP node





[Term]
id: EDAM_data:1555
name: EMBASSY domain classification
namespace: data
subset: data
def: "An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_data:1556
name: CATH class
namespace: data
subset: data
def: "Information on a protein 'class' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:1557
name: CATH architecture
namespace: data
subset: data
def: "Information on a protein 'architecture' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:1558
name: CATH topology
namespace: data
subset: data
def: "Information on a protein 'topology' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:1559
name: CATH homologous superfamily
namespace: data
subset: data
def: "Information on a protein 'homologous superfamily' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:1560
name: CATH structurally similar group
namespace: data
subset: data
def: "Information on a protein 'structurally similar group' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:1561
name: CATH functional category
namespace: data
subset: data
def: "Information on a protein 'functional category' node from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1553 ! CATH node


[Term]
id: EDAM_data:1565
name: Protein-protein interaction
namespace: data
subset: data
! alt_id: EDAM_data:2712
def: "Data on protein-protein interaction(s)." [http://edamontology.org]
comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains).
synonym: "Protein structure report (protein complex)" EXACT [http://edamontology.org]
is_a: EDAM_data:0906 ! Protein interaction
relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions


[Term]
id: EDAM_data:1566
name: Protein-ligand interaction
namespace: data
subset: data
def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org]
is_a: EDAM_data:0906 ! Protein interaction
relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions

[Term]
id: EDAM_data:1567
name: Protein-nucleic acid interaction
namespace: data
subset: data
def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org]
is_a: EDAM_data:0906 ! Protein interaction
relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions


[Term]
id: EDAM_data:2359
name: Domain-domain interaction
namespace: data
subset: data
def: "Data on protein domain-protein domain interaction(s)." [http://edamontology.org]
is_a: EDAM_data:1565 ! Protein-protein interaction

[Term]
id: EDAM_data:2378
name: Protein-motif interaction
namespace: data
subset: data
def: "Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1565 ! Protein-protein interaction

[Term]
id: EDAM_data:2360
name: Domain-domain interaction (indirect)
namespace: data
subset: data
def: "Data on indirect protein domain-protein domain interaction(s)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2359 ! Domain-domain interaction


[Term]
id: EDAM_data:2402
name: Protein-drug interaction
namespace: data
subset: data
def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org]
is_a: EDAM_data:1566 ! Protein-ligand interaction

[Term]
id: EDAM_data:2358
name: Domain-nucleic acid interaction
namespace: data
subset: data
def: "Data on protein domain-DNA/RNA interaction(s)." [http://edamontology.org]
is_a: EDAM_data:1567 ! Protein-nucleic acid interaction


[Term]
id: EDAM_data:2025
name: Michaelis Menten plot
namespace: data
subset: data
def: "A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent." [http://edamontology.org]
is_a: EDAM_data:2024 ! Enzyme kinetics data


[Term]
id: EDAM_data:2026
name: Hanes Woolf plot
namespace: data
subset: data
def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [http://edamontology.org]
is_a: EDAM_data:2024 ! Enzyme kinetics data


[Term]
id: EDAM_data:0909
name: Vmax
namespace: data
subset: data
def: "The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large." [http://edamontology.org]
is_a: EDAM_data:2024 ! Enzyme kinetics data


[Term]
id: EDAM_data:0910
name: Km
namespace: data
subset: data
def: "Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction." [http://edamontology.org]
is_a: EDAM_data:2024 ! Enzyme kinetics data

[Term]
id: EDAM_data:2720
name: Dinucleotide property
namespace: data
subset: data
def: "Physicochemical property data for one or more dinucleotides." [http://edamontology.org]
is_a: EDAM_data:2088 ! DNA base structural data



! [Term] born obsolete
! id: EDAM_data:3149 {since=beta13}
! name: Nucleic acid property (sequence)
! namespace: data
! subset: data
! def: "A non-positional property of a nucleic acid sequence." [http://edamontology.org]
! synonym: "Nucleic acid sequence property" EXACT [http://edamontology.org]
! is_obsolete: true !{since=beta13}
! consider: EDAM_data:0912 ! Nucleic acid property

[Term]
id: EDAM_data:2985
name: Nucleic acid thermodynamic data
namespace: data
subset: data
def: "A thermodynamic or kinetic property of a nucleic acid molecule." [http://edamontology.org]
synonym: "Nucleic acid property (thermodynamic or kinetic)" EXACT [http://edamontology.org]
synonym: "Nucleic acid thermodynamic property" EXACT [http://edamontology.org]
is_a: EDAM_data:0912 ! Nucleic acid property



[Term]
id: EDAM_data:1583
name: Nucleic acid melting profile
namespace: data
subset: data
def: "Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating." [http://edamontology.org]
comment: A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.
synonym: "Nucleic acid stability profile" EXACT [http://edamontology.org]
is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data

[Term]
id: EDAM_data:1584
name: Nucleic acid enthalpy
namespace: data
subset: data
def: "Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org]
is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data

[Term]
id: EDAM_data:1585
name: Nucleic acid entropy
namespace: data
subset: data
def: "Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org]
is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data


[Term]
id: EDAM_data:1586
name: Nucleic acid melting temperature
namespace: data
subset: data
def: "Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2139 ! Nucleic acid melting temperature


[Term]
id: EDAM_data:2088
name: DNA base structural data
namespace: data
subset: data
def: "Structural data for DNA base pairs or runs of bases, such as energy or angle data." [http://edamontology.org]
is_a: EDAM_data:0912 ! Nucleic acid property
is_a: EDAM_data:2086 ! Nucleic acid structure report


[Term]
id: EDAM_data:2167
name: Nucleic acid density plot
namespace: data
subset: data
def: "Density plot (of base composition) for a nucleotide sequence." [http://edamontology.org]
is_a: EDAM_data:0912 ! Nucleic acid property


[Term]
id: EDAM_data:1587
name: Nucleic acid stitch profile
namespace: data
subset: data
def: "Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA)." [http://edamontology.org]
comment: A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.
is_a: EDAM_data:1583 ! Nucleic acid melting profile

[Term]
id: EDAM_data:2958
name: Nucleic acid melting curve
namespace: data
subset: data
def: "A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org]
comment: Shows the proportion of nucleic acid which are double-stranded versus temperature.
is_a: EDAM_data:1583 ! Nucleic acid melting profile

[Term]
id: EDAM_data:2959
name: Nucleic acid probability profile
namespace: data
subset: data
def: "A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org]
comment: Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature
is_a: EDAM_data:1583 ! Nucleic acid melting profile

[Term]
id: EDAM_data:2960
name: Nucleic acid temperature profile
namespace: data
subset: data
def: "A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA)." [http://edamontology.org]
comment: Plots melting temperature versus base position.
synonym: "Melting map" EXACT [http://edamontology.org]
is_a: EDAM_data:1583 ! Nucleic acid melting profile

[Term]
id: EDAM_data:1594
name: Vienna RNA calculated energy
namespace: data
subset: data
def: "RNA calculated energy data generated by the Vienna package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1584 ! Nucleic acid enthalpy

[Term]
id: EDAM_data:1588
name: DNA base pair stacking energies data
namespace: data
subset: data
def: "DNA base pair stacking energies data." [http://edamontology.org]
is_a: EDAM_data:2088 ! DNA base structural data


[Term]
id: EDAM_data:1589
name: DNA base pair twist angle data
namespace: data
subset: data
def: "DNA base pair twist angle data." [http://edamontology.org]
is_a: EDAM_data:2088 ! DNA base structural data

[Term]
id: EDAM_data:1590
name: DNA base trimer roll angles data
namespace: data
subset: data
def: "DNA base trimer roll angles data." [http://edamontology.org]
is_a: EDAM_data:2088 ! DNA base structural data


[Term]
id: EDAM_data:1595
name: Base pairing probability matrix dotplot
namespace: data
subset: data
def: "Dotplot of RNA base pairing probability matrix." [http://edamontology.org]
comment: Such as generated by the Vienna package.
is_a: EDAM_data:2088 ! DNA base structural data


[Term]
id: EDAM_data:1598
name: Genetic code
namespace: data
subset: data
def: "A genetic code for an organism." [http://edamontology.org]
comment: A genetic code need not include detailed codon usage information.
is_a: EDAM_data:1597 ! Codon usage table


[Term]
id: EDAM_data:2865
name: Codon usage bias
namespace: data
subset: data
def: "A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences." [http://edamontology.org]
is_a: EDAM_data:0914 ! Codon usage report


[Term]
id: EDAM_data:1599
name: Codon adaptation index
namespace: data
subset: data
def: "A simple measure of synonymous codon usage bias often used to predict gene expression levels." [http://edamontology.org]
synonym: "CAI" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2865 ! Codon usage bias


[Term]
id: EDAM_data:1600
name: Codon usage bias plot
namespace: data
subset: data
def: "A plot of the synonymous codon usage calculated for windows over a nucleotide sequence." [http://edamontology.org]
synonym: "Synonymous codon usage statistic plot" EXACT [http://edamontology.org]
is_a: EDAM_data:2865 ! Codon usage bias


[Term]
id: EDAM_data:1601
name: Nc statistic
namespace: data
subset: data
def: "The effective number of codons used in a gene sequence.  This reflects how far codon usage of a gene departs from equal usage of synonymous codons." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2865 ! Codon usage bias


[Term]
id: EDAM_data:1602
name: Codon usage fraction difference
namespace: data
subset: data
def: "The differences in codon usage fractions between two codon usage tables." [http://edamontology.org]
is_a: EDAM_data:0914 ! Codon usage report

[Term]
id: EDAM_data:0917
name: Gene classification
namespace: data
subset: data
def: "A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0916 ! Gene annotation

[Term]
id: EDAM_data:0927
name: Gene annotation (linkage)
namespace: data
subset: data
def: "An informative report on the linkage of alleles." [http://edamontology.org]
is_a: EDAM_data:0916 ! Gene annotation


[Term]
id: EDAM_data:1634
name: Gene annotation (linkage disequilibrium)
namespace: data
subset: data
def: "A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome)." [http://edamontology.org]
is_a: EDAM_data:0927 ! Gene annotation (linkage)





[Term]
id: EDAM_data:0928
name: Gene expression profile
namespace: data
subset: data
def: "Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments." [http://edamontology.org]
synonym: "Gene expression pattern" EXACT [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data


[Term]
id: EDAM_data:2579
name: Expressed gene list
namespace: data
subset: data
def: "A simple summary of expressed genes." [http://edamontology.org]
synonym: "Gene annotation (expressed gene list)" EXACT [http://edamontology.org]
is_a: EDAM_data:2872 ! ID list

[Term]
id: EDAM_data:2586
name: Northern blot image
namespace: data
subset: data
def: "An image arising from a Northern Blot experiment." [http://edamontology.org]
is_a: EDAM_data:3108 ! Experimental measurement


[Term]
id: EDAM_data:1636
name: Heat map
namespace: data
subset: data
def: "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." [http://edamontology.org]
comment: A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.
is_a: EDAM_data:2967 ! Microarray image

[Term]
id: EDAM_data:2092
name: Nucleic acid features (SNP)
namespace: data
subset: data
def: "Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence." [http://edamontology.org]
comment: An SNP is an individual point mutation or substitution of a single nucleotide.
synonym: "Single nucleotide polymorphism" EXACT [http://edamontology.org]
synonym: "SNP annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)


[Term]
id: EDAM_data:2867
name: Nucleic acid features (VNTR)
namespace: data
subset: data
def: "Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence." [http://edamontology.org]
comment: VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.
synonym: "Variable number of tandem repeat polymorphism" EXACT [http://edamontology.org]
synonym: "VNTR annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)


[Term]
id: EDAM_data:2868
name: Nucleic acid features (microsatellite)
namespace: data
subset: data
def: "Annotation on a microsatellite polymorphism in a DNA sequence." [http://edamontology.org]
comment: A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.
synonym: "Microsatellite annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)


[Term]
id: EDAM_data:2869
name: Nucleic acid features (RFLP)
namespace: data
subset: data
def: "Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence." [http://edamontology.org]
comment: An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.
synonym: "RFLP annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)


[Term]
id: EDAM_data:1853
name: Chromosome annotation (aberration)
namespace: data
subset: data
def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0919 ! Gene annotation (chromosome)


[Term]
id: EDAM_data:1621
name: Pharmacogenomic annotation
namespace: data
subset: data
def: "Data on the influence of genotype on drug response." [http://edamontology.org]
comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
is_a: EDAM_data:0920 ! Genotype/phenotype annotation


[Term]
id: EDAM_data:1622
name: Disease annotation
namespace: data
subset: data
def: "An informative report on a specific disease." [http://edamontology.org]
is_a: EDAM_data:0920 ! Genotype/phenotype annotation
relationship: has_topic EDAM_topic:0634 ! Disease resources


[Term]
id: EDAM_data:2533
name: Nucleic acid features (mutation)
namespace: data
subset: data
def: "Annotation on a mutation." [http://edamontology.org]
synonym: "Mutation annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:0918 ! Nucleic acid features (variation)

[Term]
id: EDAM_data:2885
name: Nucleic acid features (polymorphism annotation)
namespace: data
subset: data
def: "Annotation on a polymorphism." [http://edamontology.org]
synonym: "Polymorphism annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:0918 ! Nucleic acid features (variation)


[Term]
id: EDAM_data:2212
name: Mutation annotation (basic)
namespace: data
subset: data
def: "Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2533 ! Nucleic acid features (mutation)


[Term]
id: EDAM_data:2213
name: Mutation annotation (prevalence)
namespace: data
subset: data
def: "An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2533 ! Nucleic acid features (mutation)


[Term]
id: EDAM_data:2214
name: Mutation annotation (prognostic)
namespace: data
subset: data
def: "An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2533 ! Nucleic acid features (mutation)


[Term]
id: EDAM_data:2215
name: Mutation annotation (functional)
namespace: data
subset: data
def: "An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2533 ! Nucleic acid features (mutation)

[Term]
id: EDAM_data:2217
name: Tumor annotation
namespace: data
subset: data
def: "An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on." [http://edamontology.org]
is_a: EDAM_data:1622 ! Disease annotation

[Term]
id: EDAM_data:1852
name: Sequence assembly component
namespace: data
subset: data
def: "A component of a larger sequence assembly." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0925 ! Sequence assembly


[Term]
id: EDAM_data:0923
name: Experiment annotation (PCR assay data)
namespace: data
subset: data
def: "Data on a PCR assay or electronic / virtual PCR." [http://edamontology.org]
synonym: "PCR assay data" EXACT [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_data:3165 {since=1.0}
name: Experiment annotation (sequencing)
namespace: data
subset: data
def: "Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis." [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation
relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis

[Term]
id: EDAM_data:0924
name: Sequence trace
namespace: data
subset: data
def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org]
comment: This is the raw data produced by a DNA sequencing machine.
is_a: EDAM_data:3108 ! Experimental measurement
is_a: EDAM_data:2887 ! Sequence record (nucleic acid)

[Term]
id: EDAM_data:0926
name: Radiation Hybrid (RH) scores
namespace: data
subset: data
def: "Radiation hybrid scores (RH) scores for one or more markers." [http://edamontology.org]
comment: Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.
is_a: EDAM_data:3108 ! Experimental measurement

[Term]
id: EDAM_data:2363
name: 2D PAGE data
namespace: data
subset: data
def: "Data concerning two-dimensional polygel electrophoresis." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0942 ! 2D PAGE image
consider: EDAM_data:2364 ! Experiment annotation (2D PAGE)

[Term]
id: EDAM_data:2838
name: Experimental data (proteomics)
namespace: data
subset: data
def: "Data concerning a proteomics experiment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry)


[Term]
id: EDAM_data:2536
name: Mass spectrometry data
namespace: data
subset: data
def: "Data concerning a mass spectrometry experiment." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
is_obsolete: true !{since=beta13}
consider: EDAM_data:0943 ! Mass spectrometry spectra
consider: EDAM_data:0944 ! Peptide mass fingerprint
consider: EDAM_data:3147 ! Experiment annotation (mass spectrometry)

[Term]
id: EDAM_data:0943
name: Mass spectrometry spectra
namespace: data
subset: data
def: "Spectra from mass spectrometry." [http://edamontology.org]
is_a: EDAM_data:3108 ! Experimental measurement
relationship: has_topic EDAM_topic:0121 ! Proteomics


[Term]
id: EDAM_data:0944
name: Peptide mass fingerprint
namespace: data
subset: data
def: "A set of peptide masses (peptide mass fingerprint) from mass spectrometry." [http://edamontology.org]
synonym: "Protein fingerprint" EXACT [http://edamontology.org]
synonym: "Peak list" EXACT [http://edamontology.org]
is_a: EDAM_data:2979 ! Peptide property
is_a: EDAM_data:3108 ! Experimental measurement
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification

[Term]
id: EDAM_data:0945
name: Peptide identification
namespace: data
subset: data
def: "Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database." [http://edamontology.org]
is_a: EDAM_data:2979 ! Peptide property
relationship: has_topic EDAM_topic:0767 ! Protein and peptide identification


[Term]
id: EDAM_data:2537
name: Protein structure raw data
namespace: data
subset: data
def: "Raw data from experimental methods for determining protein structure." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
is_a: EDAM_data:3108 ! Experimental measurement

[Term]
id: EDAM_data:0937
name: Protein X-ray crystallographic data
namespace: data
subset: data
def: "X-ray crystallography data." [http://edamontology.org]
is_a: EDAM_data:2537 ! Protein structure raw data


[Term]
id: EDAM_data:0938
name: Protein NMR data
namespace: data
subset: data
def: "Protein nuclear magnetic resonance (NMR) raw data." [http://edamontology.org]
is_a: EDAM_data:2537 ! Protein structure raw data

[Term]
id: EDAM_data:0939
name: Protein circular dichroism (CD) spectroscopic data
namespace: data
subset: data
def: "Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data." [http://edamontology.org]
is_a: EDAM_data:2537 ! Protein structure raw data

[Term]
id: EDAM_data:0940
name: Electron microscopy volume map
namespace: data
subset: data
def: "Volume map data from electron microscopy." [http://edamontology.org]
synonym: "EM volume map" EXACT [http://edamontology.org]
is_a: EDAM_data:3108 ! Experimental measurement
relationship: has_topic EDAM_topic:2226 ! Structure determination


[Term]
id: EDAM_data:0905
name: Protein interaction raw data
namespace: data
subset: data
def: "Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
is_a: EDAM_data:3108 ! Experimental measurement

[Term]
id: EDAM_data:0931
name: Experiment annotation (microarray)
namespace: data
subset: data
! alt_id: EDAM_data:3114 {since=beta13} ! Not released
def: "Information on a microarray experiment such as conditions, protocol, sample:data relationships etc." [http://edamontology.org]
comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.
synonym: "Experimental design annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation
relationship: has_topic EDAM_topic:0200 ! Microarrays

[Term]
id: EDAM_data:2866
name: Experiment annotation (Northern blot)
namespace: data
subset: data
def: "General annotation on a Northern Blot experiment." [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation

[Term]
id: EDAM_data:3147 {since=beta13}
name: Experiment annotation (mass spectrometry)
namespace: data
subset: data
def: "General annotation on a mass spectrometry experiment." [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation


[Term]
id: EDAM_data:0932
name: Oligonucleotide probe data
namespace: data
subset: data
def: "Data on oligonucleotide probes (typically for use with DNA microarrays)." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2717 ! Oligonucleotide probe annotation




[Term]
id: EDAM_data:2535
name: Sequence tag profile
namespace: data
subset: data
def: "Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment.  In all cases this is a list of short sequence tags and the number of times it is observed." [http://edamontology.org]
comment: SAGE, MPSS and SBS experiments are usually performed to study gene expression.  The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
synonym: "Sequencing-based expression profile" EXACT [http://edamontology.org]
is_a: EDAM_data:0928 ! Gene expression profile


[Term]
id: EDAM_data:0933
name: SAGE experimental data
namespace: data
subset: data
def: "Output from a serial analysis of gene expression (SAGE) experiment." [http://edamontology.org]
synonym: "Serial analysis of gene expression (SAGE) experimental data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2535 ! Sequence tag profile

[Term]
id: EDAM_data:0934
name: MPSS experimental data
namespace: data
subset: data
def: "Massively parallel signature sequencing (MPSS) data." [http://edamontology.org]
synonym: "Massively parallel signature sequencing (MPSS) experimental data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2535 ! Sequence tag profile


[Term]
id: EDAM_data:0935
name: SBS experimental data
namespace: data
subset: data
def: "Sequencing by synthesis (SBS) data." [http://edamontology.org]
synonym: "Sequencing by synthesis (SBS) experimental data" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2535 ! Sequence tag profile

[Term]
id: EDAM_data:0936
name: Sequence tag profile (with gene assignment)
namespace: data
subset: data
def: "Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers." [http://edamontology.org]
is_a: EDAM_data:2535 ! Sequence tag profile


[Term]
id: EDAM_data:0942
name: 2D PAGE image
namespace: data
subset: data
def: "Two-dimensional gel electrophoresis image." [http://edamontology.org]
synonym: "Two-dimensional gel electrophoresis image" EXACT [http://edamontology.org]
is_a: EDAM_data:2968 ! Image
is_a: EDAM_data:3108 ! Experimental measurement
relationship: has_topic EDAM_topic:0121 ! Proteomics

[Term]
id: EDAM_data:2364
name: Experiment annotation (2D PAGE)
namespace: data
subset: data
def: "An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel." [http://edamontology.org]
is_a: EDAM_data:2531 ! Experiment annotation
relationship: has_topic EDAM_topic:0121 ! Proteomics

[Term]
id: EDAM_data:2965
name: 2D PAGE image (annotated)
namespace: data
subset: data
def: "An informative report on a two-dimensional (2D PAGE) gel." [http://edamontology.org]
synonym: "2D PAGE image annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:0942 ! 2D PAGE image


[Term]
id: EDAM_data:2372
name: 2D PAGE spot (annotated)
namespace: data
subset: data
def: "An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel." [http://edamontology.org]
synonym: "2D PAGE spot annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2965 ! 2D PAGE image (annotated)

[Term]
id: EDAM_data:1646
name: Molecular weights standard fingerprint
namespace: data
subset: data
def: "Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS." [http://edamontology.org]
is_a: EDAM_data:0944 ! Peptide mass fingerprint

[Term]
id: EDAM_data:2717
name: Oligonucleotide probe annotation
namespace: data
subset: data
def: "General annotation on an oligonucleotide probe." [http://edamontology.org]
is_a: EDAM_data:3115 ! Microarray annotation
relationship: has_topic EDAM_topic:0632 ! Probes and primers



[Term]
id: EDAM_data:2966
name: Oligonucleotide probe sets annotation
namespace: data
subset: data
def: "General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set." [http://edamontology.org]
is_a: EDAM_data:2717 ! Oligonucleotide probe annotation


[Term]
id: EDAM_data:1642
name: Affymetrix probe sets library file
namespace: data
subset: data
def: "Affymetrix library file of information about which probes belong to which probe set." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation
! synonym: "CDF file" EXACT [http://edamontology.org]


[Term]
id: EDAM_data:1643
name: Affymetrix probe sets information library file
namespace: data
subset: data
def: "Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2966 ! Oligonucleotide probe sets annotation
! synonym: "GIN file" EXACT [http://edamontology.org]

[Term]
id: EDAM_data:0856
name: Sequence feature source
namespace: data
subset: data
def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org]
comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).
is_a: EDAM_data:2042 ! Evidence
is_a: EDAM_data:2914 ! Sequence features metadata


[Term]
id: EDAM_data:0859
name: Sequence signature model
namespace: data
subset: data
def: "Data files used by motif or profile methods." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0950 ! Biological model


[Term]
id: EDAM_data:0946
name: Pathway or network annotation
namespace: data
subset: data
def: "An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2984 ! Pathway or network report

[Term]
id: EDAM_data:2589
name: Hierarchy
namespace: data
subset: data
def: "A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation." [http://edamontology.org]
synonym: "Hierarchy annotation" EXACT [http://edamontology.org]
is_a: EDAM_data:2987 ! Classification


[Term]
id: EDAM_data:0904
name: Protein features (mutation)
namespace: data
subset: data
def: "Data on the effect of (typically point) mutation on protein folding, stability, structure and function." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Protein property (mutation)" EXACT [http://edamontology.org]
synonym: "Protein report (mutation)" EXACT [http://edamontology.org]
synonym: "Protein structure report (mutation)" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:0896 ! Protein report

[Term]
id: EDAM_data:0903
name: Protein folding report
namespace: data
subset: data
def: "A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Protein report (folding)" EXACT [http://edamontology.org]
synonym: "Protein property (folding)" EXACT [http://edamontology.org]
is_a: EDAM_data:0897 ! Protein property


[Term]
id: EDAM_data:1596
name: Nucleic acid folding report
namespace: data
subset: data
def: "A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.  It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
synonym: "Nucleic acid report (folding model)" EXACT [http://edamontology.org]
synonym: "Nucleic acid report (folding)" EXACT [http://edamontology.org]
is_a: EDAM_data:0912 ! Nucleic acid property


[Term]
id: EDAM_data:1344
name: MEME motif alphabet
namespace: data
subset: data
def: "Alphabet for the motifs (patterns) that MEME will search for." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:1345
name: MEME background frequencies file
namespace: data
subset: data
def: "MEME background frequencies file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:1346
name: MEME motifs directive file
namespace: data
subset: data
def: "File of directives for ordering and spacing of MEME motifs." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:1347
name: Dirichlet distribution
namespace: data
subset: data
def: "Dirichlet distribution used by hidden Markov model analysis programs." [http://edamontology.org]
is_a: EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:1348
name: HMM emission and transition counts
namespace: data
subset: data
def: "Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states." [http://edamontology.org]
is_a: EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:0947
name: Biological pathway map
namespace: data
subset: data
def: "A map (typically a diagram) of a biological pathway." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2600 ! Pathway or network


[Term]
id: EDAM_data:1656
name: Pathway or network (metabolic)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a metabolic pathway." [http://edamontology.org]
comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
is_a: EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:1657
name: Pathway or network (genetic information processing)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a genetic information processing pathway." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:2961
name: Pathway or network (gene regulation)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a gene regulatory network." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network
relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks


[Term]
id: EDAM_data:1658
name: Pathway or network (environmental information processing)
namespace: data
subset: data
def: "A report typically including a map (diagram) of an environmental information processing pathway." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network


[Term]
id: EDAM_data:1659
name: Pathway or network (signal transduction)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a signal transduction pathway." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network


[Term]
id: EDAM_data:1660
name: Pathway or network (cellular process)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a cellular process pathway." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:1661
name: Pathway or network (disease)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:1662
name: Pathway or network (drug structure relationship)
namespace: data
subset: data
def: "A report typically including a map (diagram) of drug structure relationships." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network


[Term]
id: EDAM_data:1663
name: Pathway or network (protein-protein interaction)
namespace: data
subset: data
def: "A report typically including a map (diagram) of a network of protein interactions." [http://edamontology.org]
is_a: EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:0951
name: Statistical estimate score
namespace: data
subset: data
def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org]
is_a: EDAM_data:1772 ! Score or penalty
is_a: EDAM_data:2914 ! Sequence features metadata

[Term]
id: EDAM_data:0865
name: Sequence similarity score
namespace: data
subset: data
def: "A value representing molecular sequence similarity." [http://edamontology.org]
is_a: EDAM_data:1772 ! Score or penalty


[Term]
id: EDAM_data:0888
name: Structure similarity score
namespace: data
subset: data
def: "A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison." [http://edamontology.org]
is_a: EDAM_data:1772 ! Score or penalty


[Term]
id: EDAM_data:2146
name: Threshold
namespace: data
subset: data
def: "A value that serves as a threshold for a tool (usually to control scoring or output)." [http://edamontology.org]
is_a: EDAM_data:1772 ! Score or penalty

[Term]
id: EDAM_data:1667
name: E-value
namespace: data
subset: data
def: "A simple floating point number defining the lower or upper limit of an expectation value (E-value)." [http://edamontology.org]
comment: An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.
synonym: "Expectation value" EXACT [http://edamontology.org]
is_a: EDAM_data:0951 ! Statistical estimate score

[Term]
id: EDAM_data:1668
name: Z-value
namespace: data
subset: data
def: "The z-value is the number of standard deviations a data value is above or below a mean value." [http://edamontology.org]
comment: A z-value might be specified as a threshold for reporting hits from database searches.
is_a: EDAM_data:0951 ! Statistical estimate score


[Term]
id: EDAM_data:1669
name: P-value
namespace: data
subset: data
def: "The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true." [http://edamontology.org]
comment: A z-value might be specified as a threshold for reporting hits from database searches.
is_a: EDAM_data:0951 ! Statistical estimate score

[Term]
id: EDAM_data:1412
name: Sequence identity
namespace: data
subset: data
def: "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences." [http://edamontology.org]
is_a: EDAM_data:0865 ! Sequence similarity score


[Term]
id: EDAM_data:1413
name: Sequence similarity
namespace: data
subset: data
def: "Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension." [http://edamontology.org]
comment: Data Type is float probably.
is_a: EDAM_data:0865 ! Sequence similarity score


[Term]
id: EDAM_data:2335
name: Bit score
namespace: data
subset: data
def: "A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system." [http://edamontology.org]
comment: Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.
is_a: EDAM_data:1413 ! Sequence similarity

[Term]
id: EDAM_data:1496
name: Molecular similarity score
namespace: data
subset: data
def: "A score reflecting structural similarities of two molecules." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0888 ! Structure similarity score


[Term]
id: EDAM_data:1497
name: Root-mean-square deviation
namespace: data
subset: data
def: "Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates." [http://edamontology.org]
synonym: "RMSD" EXACT [http://edamontology.org]
is_a: EDAM_data:0888 ! Structure similarity score

[Term]
id: EDAM_data:1498
name: Tanimoto similarity score
namespace: data
subset: data
def: "A measure of the similarity between two ligand fingerprints." [http://edamontology.org]
comment: A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.
is_a: EDAM_data:0888 ! Structure similarity score

[Term]
id: EDAM_data:1673
name: Swiss-Prot to PDB mapping
namespace: data
subset: data
def: "Cross-mapping of Swiss-Prot codes to PDB identifiers." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0954 ! Database cross-mapping


[Term]
id: EDAM_data:1674
name: Sequence database cross-references
namespace: data
subset: data
def: "Cross-references from a sequence record to other databases." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2093 ! Data reference


[Term]
id: EDAM_data:2337
name: Metadata
namespace: data
subset: data
! alt_id: EDAM_data:2853
def: "Data concerning or describing some core data, as distinct from the primary data that is being described.  This includes metadata on the origin, source, history, ownership or location of some thing." [http://edamontology.org]
comment: This is a broad data type and is used a placeholder for other, more specific types.
synonym: "Provenance metadata" EXACT [http://edamontology.org]
is_a: EDAM_data:2048 ! Report


[Term]
id: EDAM_data:2018
name: Annotation
namespace: data
subset: data
def: "A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it." [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:2048 ! Report



[Term]
id: EDAM_data:0948
name: Data resource definition
namespace: data
subset: data
def: "A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper." [http://edamontology.org]
is_a: EDAM_data:1883 ! Annotated URI

[Term]
id: EDAM_data:0957
name: Database metadata
namespace: data
subset: data
def: "Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc." [http://edamontology.org]
is_a: EDAM_data:3106 ! System metadata


[Term]
id: EDAM_data:2223
name: Ontology metadata
namespace: data
subset: data
def: "Data concerning a biological ontology." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:0089 ! Ontology

[Term]
id: EDAM_data:2193
name: Database entry metadata
namespace: data
subset: data
def: "Basic information on any arbitrary database entry." [http://edamontology.org]
is_a: EDAM_data:0957 ! Database metadata


[Term]
id: EDAM_data:0958
name: Tool metadata
namespace: data
subset: data
def: "Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation." [http://edamontology.org]
is_a: EDAM_data:3106 ! System metadata


[Term]
id: EDAM_data:2218
name: Server metadata
namespace: data
subset: data
def: "Basic information about a server on the web, such as an SRS server." [http://edamontology.org]
is_a: EDAM_data:3106 ! System metadata


[Term]
id: EDAM_data:0959
name: Job metadata
namespace: data
subset: data
def: "Textual metadata on a submitted or completed job." [http://edamontology.org]
xref: Moby:PDGJOB
is_a: EDAM_data:3106 ! System metadata

[Term]
id: EDAM_data:0960
name: User metadata
namespace: data
subset: data
def: "Textual metadata on a software author or end-user, for example a person or other software." [http://edamontology.org]
is_a: EDAM_data:3106 ! System metadata

[Term]
id: EDAM_data:3106 {since=beta13}
name: System metadata
namespace: data
subset: data
def: "Metadata concerning the software, hardware or other aspects of a computer system." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata


[Term]
id: EDAM_data:0583
name: Directory metadata
namespace: data
subset: data
def: "A directory on disk from which files are read." [http://edamontology.org]
is_a: EDAM_data:3106 ! System metadata

[Term]
id: EDAM_data:0953
name: Version information
namespace: data
subset: data
def: "Information on a version of software or data, for example name, version number and release date." [http://edamontology.org]
synonym: "Version" EXACT [http://usefulinc.com/ns/doap#Version]
synonym: "version identifier" NARROW [http://semanticscience.org/resource/SIO_000653]
synonym: "version name or number" NARROW [http://purl.obolibrary.org/obo/IAO_0000129]
synonym: "development status" NARROW [http://www.ebi.ac.uk/swo/maturity/SWO_9000061] {note="Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records."}
is_a: EDAM_data:2337 ! Metadata

[Term]
id: EDAM_data:2724
name: Embryo annotation
namespace: data
subset: data
def: "Annotation on an embryo or concerning embryological development." [http://edamontology.org]
is_a: EDAM_data:2530 ! Organism annotation
relationship: has_topic EDAM_topic:3065 ! Embryology resources

[Term]
id: EDAM_data:1664
name: MIRIAM datatype
namespace: data
subset: data
def: "An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources." [http://edamontology.org]
comment: A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
is_a: EDAM_data:0948 ! Data resource definition


[Term]
id: EDAM_data:2875
name: DRCAT resource
namespace: data
subset: data
def: "An entry (resource) from the DRCAT bioinformatics resource catalogue." [http://edamontology.org]
is_a: EDAM_data:0948 ! Data resource definition


[Term]
id: EDAM_data:0952
name: EMBOSS database resource definition
namespace: data
subset: data
def: "Resource definition for an EMBOSS database." [http://edamontology.org]
is_a: EDAM_data:0957 ! Database metadata



[Term]
id: EDAM_data:1675
name: Job status
namespace: data
subset: data
def: "Metadata on the status of a submitted job." [http://edamontology.org]
comment: Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
is_a: EDAM_data:0959 ! Job metadata


[Term]
id: EDAM_data:1678
name: Tool log
namespace: data
subset: data
def: "A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages." [http://edamontology.org]
is_a: EDAM_data:0959 ! Job metadata

[Term]
id: EDAM_data:1677
name: Job type
namespace: data
subset: data
def: "A label (text token) describing the type of job, for example interactive or non-interactive." [http://edamontology.org]
is_a: EDAM_data:2100 ! Type



[Term]
id: EDAM_data:1679
name: DaliLite log file
namespace: data
subset: data
def: "DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log


[Term]
id: EDAM_data:1680
name: STRIDE log file
namespace: data
subset: data
def: "STRIDE log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log


[Term]
id: EDAM_data:1681
name: NACCESS log file
namespace: data
subset: data
def: "NACCESS log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1682
name: EMBOSS wordfinder log file
namespace: data
subset: data
def: "EMBOSS wordfinder log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1683
name: EMBOSS domainatrix log file
namespace: data
subset: data
def: "EMBOSS (EMBASSY) domainatrix application log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1684
name: EMBOSS sites log file
namespace: data
subset: data
def: "EMBOSS (EMBASSY) sites application log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1685
name: EMBOSS supermatcher error file
namespace: data
subset: data
def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1686
name: EMBOSS megamerger log file
namespace: data
subset: data
def: "EMBOSS megamerger log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1687
name: EMBOSS whichdb log file
namespace: data
subset: data
def: "EMBOSS megamerger log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log

[Term]
id: EDAM_data:1688
name: EMBOSS vectorstrip log file
namespace: data
subset: data
def: "EMBOSS vectorstrip log file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1678 ! Tool log





[Term]
id: EDAM_data:1670
name: Database version information
namespace: data
subset: data
def: "Information on a database (or ontology) version, for example name, version number and release date." [http://edamontology.org]
synonym: "Ontology version information" EXACT [http://edamontology.org]
is_a: EDAM_data:0953 ! Version information
is_a: EDAM_data:0957 ! Database metadata


[Term]
id: EDAM_data:2090
name: Database entry version information
namespace: data
subset: data
def: "Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on." [http://edamontology.org]
is_a: EDAM_data:0953 ! Version information
is_a: EDAM_data:2193 ! Database entry metadata


[Term]
id: EDAM_data:1671
name: Tool version information
namespace: data
subset: data
def: "Information on an application version, for example name, version number and release date." [http://edamontology.org]
is_a: EDAM_data:0953 ! Version information
is_a: EDAM_data:0958 ! Tool metadata


[Term]
id: EDAM_data:1771
name: Sequence version information
namespace: data
subset: data
def: "Information on an molecular sequence version." [http://edamontology.org]
is_a: EDAM_data:0953 ! Version information
is_a: EDAM_data:0855 ! Sequence metadata

[Term]
id: EDAM_data:2041
name: Genome version information
namespace: data
subset: data
def: "Information on a genome version." [http://edamontology.org]
is_a: EDAM_data:0953 ! Version information
is_a: EDAM_data:2711 ! Genome metadata

[Term]
id: EDAM_data:1672
name: CATH version information
namespace: data
subset: data
def: "Information on a version of the CATH database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1670 ! Database version information


[Term]
id: EDAM_data:1047
name: URI
namespace: data
subset: data
def: "A string of characters that name or otherwise identify a resource on the Internet." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter



[Term]
id: EDAM_data:2079
name: Search parameter
namespace: data
subset: data
def: "Some simple value controlling a search operation, typically a search of a database." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter



[Term]
id: EDAM_data:2534
name: Sequence parameter
namespace: data
subset: data
def: "A parameter concerning calculations on molecular sequences." [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter

[Term]
id: EDAM_data:2130
name: Sequence profile type
namespace: data
subset: data
def: "A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter
is_a: EDAM_data:2100 ! Type


[Term]
id: EDAM_data:2023
name: Sequence mask parameter
namespace: data
subset: data
def: "Data used to replace (mask) characters in a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter


[Term]
id: EDAM_data:0853
name: DNA sense specification
namespace: data
subset: data
def: "The strand of a DNA sequence (forward or reverse)." [http://edamontology.org]
comment: The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.
synonym: "DNA strand specification" EXACT [http://edamontology.org]
synonym: "Strand" EXACT [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter
is_a: EDAM_data:2914 ! Sequence features metadata


[Term]
id: EDAM_data:2126
name: Translation frame specification
namespace: data
subset: data
def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter


[Term]
id: EDAM_data:2336
name: Translation phase specification
namespace: data
subset: data
def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org]
synonym: "Phase" EXACT [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter
is_a: EDAM_data:2914 ! Sequence features metadata


[Term]
id: EDAM_data:1014
name: Sequence position specification
namespace: data
subset: data
def: "A specification (partial or complete) of one or more positions or regions of a molecular sequence or map." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter


[Term]
id: EDAM_data:0854
name: Sequence length specification
namespace: data
subset: data
def: "A specification of sequence length(s)." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter


[Term]
id: EDAM_data:2357
name: Protein signature type
namespace: data
subset: data
def: "A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter
is_a: EDAM_data:2100 ! Type

[Term]
id: EDAM_data:0864
name: Sequence alignment parameter
namespace: data
subset: data
def: "Some simple value controlling a sequence alignment (or similar 'match') operation." [http://edamontology.org]
is_a: EDAM_data:2534 ! Sequence parameter

[Term]
id: EDAM_data:1120
name: Sequence alignment type
namespace: data
subset: data
def: "A label (text token) describing the type of a sequence alignment." [http://edamontology.org]
comment: Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
is_a: EDAM_data:0864 ! Sequence alignment parameter
is_a: EDAM_data:2100 ! Type



[Term]
id: EDAM_data:1052
name: URL
namespace: data
subset: data
! alt_id: EDAM_data:1054
! alt_id: EDAM_data:1168
! alt_id: EDAM_data:1169
def: "A Uniform Resource Locator (URL)." [http://edamontology.org]
xref: Moby:URL
xref: Moby:Link
is_a: EDAM_data:1047 ! URI


[Term]
id: EDAM_data:1053
name: URN
namespace: data
subset: data
def: "A Uniform Resource Name (URN)." [http://edamontology.org]
is_a: EDAM_data:1047 ! URI


[Term]
id: EDAM_data:1055
name: LSID
namespace: data
subset: data
def: "A Life Science Identifier (LSID) - a unique identifier of some data." [http://edamontology.org]
comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
synonym: "Life Science Identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1053 ! URN

[Term]
id: EDAM_data:0968
name: Keyword
namespace: data
subset: data
def: "Keyword(s) or phrase(s) used (typically) for text-searching purposes." [http://edamontology.org]
comment: Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.
xref: Moby:Global_Keyword
xref: Moby:QueryString
xref: Moby:Wildcard_Query
xref: Moby:BooleanQueryString
is_a: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:2022
name: Vienna RNA structural data
namespace: data
subset: data
def: "Data used by the Vienna RNA analysis package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:2134
name: Results sort order
namespace: data
subset: data
def: "A control of the order of data that is output, for example the order of sequences in an alignment." [http://edamontology.org]
is_a: EDAM_data:2079 ! Search parameter

[Term]
id: EDAM_data:2135
name: Toggle
namespace: data
subset: data
def: "A simple parameter that is a toggle (boolean value), typically a control for a modal tool." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:2139
name: Nucleic acid melting temperature
namespace: data
subset: data
def: "A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate." [http://edamontology.org]
synonym: "Melting temperature" EXACT [http://edamontology.org]
is_a: EDAM_data:2985 ! Nucleic acid thermodynamic data


[Term]
id: EDAM_data:2140
name: Concentration
namespace: data
subset: data
def: "The concentration of a chemical compound." [http://edamontology.org]
is_a: EDAM_data:2050 ! Molecular property (general)

[Term]
id: EDAM_data:2151
name: Color
namespace: data
subset: data
def: "Specification of one or more colors." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2152 ! Rendering parameter


[Term]
id: EDAM_data:2152
name: Rendering parameter
namespace: data
subset: data
def: "A parameter that is used to control rendering (drawing) to a device or image." [http://edamontology.org]
synonym: "Graphics parameter" EXACT [http://edamontology.org]
synonym: "Graphical parameter" EXACT [http://edamontology.org]
is_a: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:3105 {since=beta13}
name: Geotemporal metadata
namespace: data
subset: data
def: "Basic information concerning geographical location or time." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata

[Term]
id: EDAM_data:2156
name: Date
namespace: data
subset: data
def: "A temporal date." [http://edamontology.org]
is_a: EDAM_data:3105 ! Geotemporal metadata


[Term]
id: EDAM_data:1693
name: Number of iterations
namespace: data
subset: data
def: "Number of iterations of an algorithm." [http://edamontology.org]
is_a: EDAM_data:2079 ! Search parameter

[Term]
id: EDAM_data:1694
name: Number of output entities
namespace: data
subset: data
def: "Number of entities (for example database hits, sequences, alignments etc) to write to an output file." [http://edamontology.org]
is_a: EDAM_data:2079 ! Search parameter



! Possible values include: 'SC' (score) or 'RF' (rank), pvalue (sort by increasing P-value (probability). i.e. most statistically significant hits given first), count (sort hits by increasing number of submatches (for example HSP) in each hit, score (sort hits in order of increasing score



[Term]
id: EDAM_data:1695
name: Hit sort order
namespace: data
subset: data
def: "Controls the order of hits (reported matches) in an output file from a database search." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2134 ! Results sort order

[Term]
id: EDAM_data:0851
name: Sequence mask character
namespace: data
subset: data
def: "A character used to replace (mask) other characters in a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:2023 ! Sequence mask parameter

[Term]
id: EDAM_data:0852
name: Sequence mask type
namespace: data
subset: data
def: "A label (text token) describing the type of sequence masking to perform." [http://edamontology.org]
comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
is_a: EDAM_data:2023 ! Sequence mask parameter
is_a: EDAM_data:2100 ! Type


[Term]
id: EDAM_data:1016
name: Sequence position
namespace: data
subset: data
def: "A position of a single point (base or residue) in a sequence, or part of such a specification." [http://edamontology.org]
synonym: "sequence_location" RELATED [SO:0000735]
xref: WHATIF: number
xref: WHATIF: PDBx_atom_site
is_a: EDAM_data:1014 ! Sequence position specification
! _atom_site.id in PDBML

[Term]
id: EDAM_data:2145
name: Sequence offset
namespace: data
subset: data
def: "An offset for a single-point sequence position." [http://edamontology.org]
is_a: EDAM_data:1016 ! Sequence position
is_a: EDAM_data:2914 ! Sequence features metadata

[Term]
id: EDAM_data:1017
name: Sequence range
namespace: data
subset: data
def: "Specification of range(s) of sequence positions." [http://edamontology.org]
is_a: EDAM_data:1014 ! Sequence position specification

[Term]
id: EDAM_data:2012
name: Map position
namespace: data
subset: data
! alt_id: EDAM_data:1894
def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval." [http://edamontology.org]
comment: This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome.
synonym: "Locus" EXACT [http://edamontology.org]
! synonym: An ontology concept covering the different types of position/locus RELATED [...]
xref: Moby:GCP_MapPoint
xref: Moby:GCP_MapPosition
xref: Moby:HitPosition
xref: Moby:GenePosition
xref: Moby:MapPosition
xref: Moby:Position
xref: Moby:GCP_MapInterval
xref: Moby:Locus
is_a: EDAM_data:1016 ! Sequence position
is_a: EDAM_data:1017 ! Sequence range
is_a: EDAM_data:2019 ! Map attribute
! _atom_site.id in PDBML

[Term]
id: EDAM_data:2216
name: Codon number
namespace: data
subset: data
def: "The number of a codon, for instance, at which a mutation is located." [http://edamontology.org]
is_a: EDAM_data:1016 ! Sequence position

[Term]
id: EDAM_data:1742
name: PDB residue number
namespace: data
subset: data
def: "A residue identifier (a string) from a PDB file." [http://edamontology.org]
xref: WHATIF: pdb_number
is_a: EDAM_data:1016 ! Sequence position
! PDB_residue_no in PDBML

[Term]
id: EDAM_data:1856
name: PDB insertion code
namespace: data
subset: data
def: "An insertion code (part of the residue number) for an amino acid residue from a PDB file." [http://edamontology.org]
xref: WHATIF: insertion_code
is_a: EDAM_data:1016 ! Sequence position
! pdbx_PDB_ins_code in PDBML


[Term]
id: EDAM_data:1906
name: Quantitative trait locus
namespace: data
subset: data
def: "A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment)." [http://edamontology.org]
comment: A QTL sometimes but does not necessarily correspond to a gene.
synonym: "QTL" EXACT [http://edamontology.org]
xref: Moby:SO_QTL
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2012 ! Map position

[Term]
id: EDAM_data:1249
name: Sequence length
namespace: data
subset: data
def: "The size (length) of a sequence, subsequence or region in a sequence." [http://edamontology.org]
is_a: EDAM_data:0854 ! Sequence length specification

[Term]
id: EDAM_data:1252
name: Sequence length range
namespace: data
subset: data
def: "Specification of range(s) of length of sequences." [http://edamontology.org]
is_a: EDAM_data:0854 ! Sequence length specification

[Term]
id: EDAM_data:1250
name: Word size
namespace: data
subset: data
def: "Size of a sequence word." [http://edamontology.org]
comment: Word size is used for example in word-based sequence database search methods.
synonym: "Word length" EXACT [http://edamontology.org]
is_a: EDAM_data:1249 ! Sequence length


[Term]
id: EDAM_data:1251
name: Window size
namespace: data
subset: data
def: "Size of a sequence window." [http://edamontology.org]
comment: A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.
is_a: EDAM_data:1249 ! Sequence length


[Term]
id: EDAM_data:2141
name: Window step size
namespace: data
subset: data
def: "Size of the incremental 'step' a sequence window is moved over a sequence." [http://edamontology.org]
is_a: EDAM_data:1249 ! Sequence length

[Term]
id: EDAM_data:1125
name: Comparison matrix type
namespace: data
subset: data
def: "A label (text token) describing the type of a comparison matrix." [http://edamontology.org]
comment: For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.
example: "blosum" "pam" "gonnet" "id"
synonym: "Substitution matrix type" EXACT [http://edamontology.org]
is_a: EDAM_data:0864 ! Sequence alignment parameter
is_a: EDAM_data:2100 ! Type


[Term]
id: EDAM_data:1394
name: Alignment score or penalty
namespace: data
subset: data
def: "A simple floating point number defining the penalty for opening or extending a gap in an alignment." [http://edamontology.org]
is_a: EDAM_data:0864 ! Sequence alignment parameter
is_a: EDAM_data:1772 ! Score or penalty


[Term]
id: EDAM_data:1395
name: Score end gaps control
namespace: data
subset: data
def: "Whether end gaps are scored or not." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:1396
name: Aligned sequence order
namespace: data
subset: data
def: "Controls the order of sequences in an output sequence alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2134 ! Results sort order

[Term]
id: EDAM_data:2136
name: Sequence width
namespace: data
subset: data
def: "The width of an output sequence or alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1249 ! Sequence length

[Term]
id: EDAM_data:2137
name: Gap penalty
namespace: data
subset: data
def: "A penalty for introducing or extending a gap in an alignment." [http://edamontology.org]
is_a: EDAM_data:1394 ! Alignment score or penalty

[Term]
id: EDAM_data:1401
name: Match reward score
namespace: data
subset: data
def: "The score for a 'match' used in various sequence database search applications with simple scoring schemes." [http://edamontology.org]
is_a: EDAM_data:1394 ! Alignment score or penalty


[Term]
id: EDAM_data:1402
name: Mismatch penalty score
namespace: data
subset: data
def: "The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes." [http://edamontology.org]
is_a: EDAM_data:1394 ! Alignment score or penalty


[Term]
id: EDAM_data:1403
name: Drop off score
namespace: data
subset: data
def: "This is the threshold drop in score at which extension of word alignment is halted." [http://edamontology.org]
is_a: EDAM_data:1394 ! Alignment score or penalty


[Term]
id: EDAM_data:1397
name: Gap opening penalty
namespace: data
subset: data
def: "A penalty for opening a gap in an alignment." [http://edamontology.org]
is_a: EDAM_data:2137 ! Gap penalty


[Term]
id: EDAM_data:1398
name: Gap extension penalty
namespace: data
subset: data
def: "A penalty for extending a gap in an alignment." [http://edamontology.org]
is_a: EDAM_data:2137 ! Gap penalty


[Term]
id: EDAM_data:1399
name: Gap separation penalty
namespace: data
subset: data
def: "A penalty for gaps that are close together in an alignment." [http://edamontology.org]
is_a: EDAM_data:2137 ! Gap penalty


[Term]
id: EDAM_data:1400
name: Terminal gap penalty
namespace: data
subset: data
def: "A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1410 ! Terminal gap opening penalty
consider: EDAM_data:1411 ! Terminal gap extension penalty

[Term]
id: EDAM_data:1404
name: Gap opening penalty (integer)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1397 ! Gap opening penalty


[Term]
id: EDAM_data:1405
name: Gap opening penalty (float)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for opening a gap in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1397 ! Gap opening penalty

[Term]
id: EDAM_data:1406
name: Gap extension penalty (integer)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1398 ! Gap extension penalty


[Term]
id: EDAM_data:1407
name: Gap extension penalty (float)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for extending a gap in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1398 ! Gap extension penalty

[Term]
id: EDAM_data:1408
name: Gap separation penalty (integer)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1399 ! Gap separation penalty


[Term]
id: EDAM_data:1409
name: Gap separation penalty (float)
namespace: data
subset: data
def: "A simple floating point number defining the penalty for gaps that are close together in an alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1399 ! Gap separation penalty


[Term]
id: EDAM_data:1410
name: Terminal gap opening penalty
namespace: data
subset: data
def: "A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org]
is_a: EDAM_data:1397 ! Gap opening penalty

[Term]
id: EDAM_data:1411
name: Terminal gap extension penalty
namespace: data
subset: data
def: "A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences." [http://edamontology.org]
is_a: EDAM_data:1398 ! Gap extension penalty

[Term]
id: EDAM_data:2007
name: UniProt keyword
namespace: data
subset: data
def: "A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database." [http://edamontology.org]
xref: Moby_namespace:SP_KW
xref: http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW
is_a: EDAM_data:0968 ! Keyword


[Term]
id: EDAM_data:1877
name: Synonym
namespace: data
subset: data
def: "An alternative for a word." [http://edamontology.org]
synonym: "Alternative name" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0968 ! Keyword


[Term]
id: EDAM_data:1878
name: Misspelling
namespace: data
subset: data
def: "A common misspelling of a word." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0968 ! Keyword


[Term]
id: EDAM_data:1879
name: Acronym
namespace: data
subset: data
def: "An abbreviation of a phrase or word." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0968 ! Keyword


[Term]
id: EDAM_data:1880
name: Misnomer
namespace: data
subset: data
def: "A term which is likely to be misleading of its meaning." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0968 ! Keyword

[Term]
id: EDAM_data:1591
name: Vienna RNA parameters
namespace: data
subset: data
def: "RNA parameters used by the Vienna package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter

[Term]
id: EDAM_data:1592
name: Vienna RNA structure constraints
namespace: data
subset: data
def: "Structure constraints used by the Vienna package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter


[Term]
id: EDAM_data:1593
name: Vienna RNA concentration data
namespace: data
subset: data
def: "RNA concentration data used by the Vienna package." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2527 ! Parameter

[Term]
id: EDAM_data:1696
name: Drug annotation
namespace: data
subset: data
def: "An informative report on a specific drug." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation
relationship: has_topic EDAM_topic:0620 ! Drugs and targets

[Term]
id: EDAM_data:2400
name: Toxin annotation
namespace: data
subset: data
def: "An informative report on a specific toxin." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation

[Term]
id: EDAM_data:2240
name: Heterogen annotation
namespace: data
subset: data
def: "An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation


[Term]
id: EDAM_data:2726
name: Inhibitor annotation
namespace: data
subset: data
def: "An informative report on one or more small molecules that are enzyme inhibitors." [http://edamontology.org]
is_a: EDAM_data:0962 ! Small molecule annotation

[Term]
id: EDAM_data:2396
name: Fungi annotation (anamorph)
namespace: data
subset: data
def: "An informative report on a specific fungus anamorph." [http://edamontology.org]
is_a: EDAM_data:2395 ! Fungi annotation

[Term]
id: EDAM_data:2142
name: EMBOSS graph
namespace: data
subset: data
def: "An image of a graph generated by the EMBOSS suite." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2968 ! Image


[Term]
id: EDAM_data:1707
name: Phylogenetic tree image
namespace: data
subset: data
def: "An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information." [http://edamontology.org]
comment: See also 'Phylogenetic tree'
is_a: EDAM_data:2968 ! Image
is_a: EDAM_data:1438 ! Phylogenetic tree report


[Term]
id: EDAM_data:1708
name: RNA secondary structure image
namespace: data
subset: data
def: "Image of RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org]
is_a: EDAM_data:2880 ! Secondary structure image

[Term]
id: EDAM_data:1709
name: Protein secondary structure image
namespace: data
subset: data
def: "Image of protein secondary structure." [http://edamontology.org]
is_a: EDAM_data:2880 ! Secondary structure image
is_a: EDAM_data:2956 ! Protein secondary structure report

[Term]
id: EDAM_data:1710
name: Structure image
namespace: data
subset: data
! alt_id: EDAM_data:2604
def: "Image of one or more molecular tertiary (3D) structures." [http://edamontology.org]
is_a: EDAM_data:2085 ! Structure report
is_a: EDAM_data:2968 ! Image

[Term]
id: EDAM_data:2880
name: Secondary structure image
namespace: data
subset: data
def: "Image of one or more molecular secondary structures." [http://edamontology.org]
is_a: EDAM_data:2881 ! Secondary structure report

[Term]
id: EDAM_data:1711
name: Sequence alignment image
namespace: data
subset: data
def: "Image of two or more aligned molecular sequences possibly annotated with alignment features." [http://edamontology.org]
is_a: EDAM_data:2968 ! Image
is_a: EDAM_data:0867 ! Sequence alignment report


[Term]
id: EDAM_data:2168
name: Sequence trace image
namespace: data
subset: data
def: "Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases)." [http://edamontology.org]
is_a: EDAM_data:2969 ! Sequence image

[Term]
id: EDAM_data:2969
name: Sequence image
namespace: data
subset: data
def: "Image of a molecular sequence, possibly with sequence features or properties shown." [http://edamontology.org]
is_a: EDAM_data:2968 ! Image
is_a: EDAM_data:2955 ! Sequence report


[Term]
id: EDAM_data:1712
name: Structure image (small molecule)
namespace: data
subset: data
def: "An image of the structure of a small chemical compound." [http://edamontology.org]
comment: The molecular identifier and formula are typically included.
synonym: "Chemical structure image" EXACT [http://edamontology.org]
synonym: "Small molecule structure image" EXACT [http://edamontology.org]
is_a: EDAM_data:1710 ! Structure image
is_a: EDAM_data:0962 ! Small molecule annotation


[Term]
id: EDAM_data:2992
name: Protein structure image
namespace: data
subset: data
def: "An image of protein structure." [http://edamontology.org]
synonym: "Structure image (protein)" EXACT [http://edamontology.org]
is_a: EDAM_data:1710 ! Structure image
is_a: EDAM_data:3153 ! Protein image


[Term]
id: EDAM_data:3154 {since=beta13}
name: Protein alignment
namespace: data
subset: data
def: "An alignment of protein sequences and/or structures." [http://edamontology.org]
is_a: EDAM_data:0896 ! Protein report
is_a: EDAM_data:1916 ! Alignment

[Term]
id: EDAM_data:3153 {since=beta13}
name: Protein image
namespace: data
subset: data
def: "An image of a protein." [http://edamontology.org]
is_a: EDAM_data:0896 ! Protein report


[Term]
id: EDAM_data:1713
name: Fate map
namespace: data
subset: data
def: " A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development." [http://edamontology.org]
is_a: EDAM_data:2724 ! Embryo annotation


[Term]
id: EDAM_data:2967
name: Microarray image
namespace: data
subset: data
! alt_id: EDAM_data:1635
def: "An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data." [http://edamontology.org]
synonym: "Gene expression image" EXACT [http://edamontology.org]
is_a: EDAM_data:2603 ! Microarray data
is_a: EDAM_data:2968 ! Image
relationship: has_topic EDAM_topic:0200 ! Microarrays

[Term]
id: EDAM_data:1714
name: Microarray spots image
namespace: data
subset: data
def: "An image of spots from a microarray experiment." [http://edamontology.org]
is_a: EDAM_data:2967 ! Microarray image
is_a: EDAM_data:3108 ! Experimental measurement

[Term]
id: EDAM_data:2162
name: Helical wheel
namespace: data
subset: data
def: "An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties." [http://edamontology.org]
is_a: EDAM_data:1709 ! Protein secondary structure image


[Term]
id: EDAM_data:2163
name: Helical net
namespace: data
subset: data
def: "An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix." [http://edamontology.org]
comment: Useful for highlighting amphipathicity and other properties.
is_a: EDAM_data:1709 ! Protein secondary structure image

[Term]
id: EDAM_data:2308
name: Virus annotation (taxonomy)
namespace: data
subset: data
def: "An informative report on the taxonomy of a specific virus." [http://edamontology.org]
is_a: EDAM_data:2307 ! Virus annotation

[Term]
id: EDAM_data:0582
name: Ontology
namespace: data
subset: data
! alt_id: EDAM_data:0829
! alt_id: EDAM_data:0830
! alt_id: EDAM_data:0834
! alt_id: EDAM_data:0836
! alt_id: EDAM_data:0837
! alt_id: EDAM_data:0838
! alt_id: EDAM_data:0839
! alt_id: EDAM_data:0840
! alt_id: EDAM_data:2221
def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org]
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0089 ! Ontology


[Term]
id: EDAM_data:2858
name: Ontology concept
namespace: data
subset: data
def: "A concept from a biological ontology." [http://edamontology.org]
comment: This includes any fields from the concept definition such as concept name, definition, comments and so on.
is_a: EDAM_data:3031 ! Core data
relationship: has_topic EDAM_topic:0089 ! Ontology


[Term]
id: EDAM_data:0966
name: Ontology term
namespace: data
subset: data
def: "A term (name) from an ontology." [http://edamontology.org]
is_a: EDAM_data:0967 ! Ontology concept metadata


[Term]
id: EDAM_data:0967
name: Ontology concept metadata
namespace: data
subset: data
def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org]
is_a: EDAM_data:2337 ! Metadata
relationship: has_topic EDAM_topic:0089 ! Ontology


[Term]
id: EDAM_data:1715
name: BioPax
namespace: data
subset: data
def: "A term from the BioPax ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1716
name: GO
namespace: data
subset: data
def: "A term definition from The Gene Ontology (GO)." [http://edamontology.org]
synonym: "Gene Ontology term" EXACT [http://edamontology.org]
xref: Moby:GO_Term
xref: Moby:GOTerm
xref: Moby:Annotated_GO_Term
xref: Moby:Annotated_GO_Term_With_Probability
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1717
name: MeSH
namespace: data
subset: data
def: "A term from the MeSH vocabulary." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1718
name: HGNC
namespace: data
subset: data
def: "A term from the HGNC controlled vocabulary." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1719
name: NCBI taxonomy vocabulary
namespace: data
subset: data
def: "A term from the NCBI taxonomy vocabulary." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1720
name: Plant ontology term
namespace: data
subset: data
def: "A term from the Plant Ontology (PO)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1721
name: UMLS
namespace: data
subset: data
def: "A term from the UMLS vocabulary." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1722
name: FMA
namespace: data
subset: data
def: "A term from Foundational Model of Anatomy." [http://edamontology.org]
comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1723
name: EMAP
namespace: data
subset: data
def: "A term from the EMAP mouse ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1724
name: ChEBI
namespace: data
subset: data
def: "A term from the ChEBI ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1725
name: MGED
namespace: data
subset: data
def: "A term from the MGED ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term

[Term]
id: EDAM_data:1726
name: myGrid
namespace: data
subset: data
def: "A term from the myGrid ontology." [http://edamontology.org]
comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0966 ! Ontology term


[Term]
id: EDAM_data:1727
name: GO (biological process)
namespace: data
subset: data
def: "A term definition for a biological process from the Gene Ontology (GO)." [http://edamontology.org]
comment: Data Type is an enumerated string.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2858 ! Ontology concept

[Term]
id: EDAM_data:1728
name: GO (molecular function)
namespace: data
subset: data
def: "A term definition for a molecular function from the Gene Ontology (GO)." [http://edamontology.org]
comment: Data Type is an enumerated string.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2858 ! Ontology concept

[Term]
id: EDAM_data:1729
name: GO (cellular component)
namespace: data
subset: data
def: "A term definition for a cellular component from the Gene Ontology (GO)." [http://edamontology.org]
comment: Data Type is an enumerated string.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2858 ! Ontology concept


[Term]
id: EDAM_data:1730
name: Ontology relation type
namespace: data
subset: data
def: "A relation type defined in an ontology." [http://edamontology.org]
is_a: EDAM_data:0967 ! Ontology concept metadata

[Term]
id: EDAM_data:1731
name: Ontology concept definition
namespace: data
subset: data
def: "The definition of a concept from an ontology." [http://edamontology.org]
is_a: EDAM_data:0967 ! Ontology concept metadata

[Term]
id: EDAM_data:1732
name: Ontology concept comment
namespace: data
subset: data
def: "A comment on a concept from an ontology." [http://edamontology.org]
is_a: EDAM_data:0967 ! Ontology concept metadata

[Term]
id: EDAM_data:1733
name: Ontology concept reference
namespace: data
subset: data
def: "Reference for a concept from an ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2093 ! Data reference


[Term]
id: EDAM_data:1738
name: doc2loc document information
namespace: data
subset: data
def: "Information on a published article provided by the doc2loc program." [http://edamontology.org]
comment: The doc2loc output includes the url, format, type and availability code of a document for every service provider.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0970 ! Bibliographic reference


[Term]
id: EDAM_data:2177
name: Exactly 1
namespace: data
subset: data
def: "A single thing." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:2178
name: 1 or more
namespace: data
subset: data
def: "One or more things." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:2179
name: Exactly 2
namespace: data
subset: data
def: "Exactly two things." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}


[Term]
id: EDAM_data:2180
name: 2 or more
namespace: data
subset: data
def: "Two or more things." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}



!
! Identifier
!


[Term]
id: EDAM_data:1121
name: BLAST sequence alignment type
namespace: identifier
subset: identifiers
subset: data
def: "The type of a BLAST sequence alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1120 ! Sequence alignment type

[Term]
id: EDAM_data:0974
name: Entity identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a biological entity or phenomenon." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:0975
name: Data resource identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a data resource." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:0978
name: Discrete entity identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier


[Term]
id: EDAM_data:0979
name: Entity feature identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:0980
name: Entity collection identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a collection of discrete biological entities." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:0981
name: Phenomenon identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a physical, observable biological occurrence or event." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier


[Term]
id: EDAM_data:2091
name: Accession
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:2862
def: "A persistent (stable) and unique identifier, typically identifying an object (entry) from a database." [http://edamontology.org]
synonym: "information entity identifier" BROAD [http://semanticscience.org/resource/SIO_000731]
synonym: "unique identifier" BROAD [http://semanticscience.org/resource/SIO_000675]
is_a: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:2099
name: Name
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:2863
def: "A name of a thing, which need not necessarily uniquely identify it." [http://edamontology.org]
synonym: "Symbolic name" EXACT [http://edamontology.org]
synonym: "name" EXACT [http://usefulinc.com/ns/doap#name]
synonym: "name" EXACT [http://semanticscience.org/resource/SIO_000116]
synonym: "label" BROAD [http://www.w3.org/2000/01/rdf-schema#label] {note="Almost exact, but focusing on human readability and not on identification."}
is_a: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:0976
name: Identifier (typed)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier that identifies a particular type of data." [http://edamontology.org]
comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information.  This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
is_a: EDAM_data:0842 ! Identifier

[Term]
id: EDAM_data:2109
name: Identifier (hybrid)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier that is re-used for data objects of fundamentally different types (typically served from a single database)." [http://edamontology.org]
comment: This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
is_a: EDAM_data:0842 ! Identifier



[Term]
id: EDAM_data:0977
name: Tool identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a bioinformatics tool, e.g. an application or web service." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:1190
name: Tool name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a computer package, application, method or function." [http://edamontology.org]
is_a: EDAM_data:0977 ! Tool identifier


[Term]
id: EDAM_data:1191
name: Tool name (signature)
namespace: identifier
subset: identifiers
subset: data
def: "The unique name of a signature (sequence classifier) method." [http://edamontology.org]
comment: Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.
is_a: EDAM_data:1190 ! Tool name

[Term]
id: EDAM_data:1192
name: Tool name (BLAST)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a BLAST tool." [http://edamontology.org]
comment: This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.
synonym: "BLAST name" EXACT [http://edamontology.org]
is_a: EDAM_data:1190 ! Tool name

[Term]
id: EDAM_data:1193
name: Tool name (FASTA)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a FASTA tool." [http://edamontology.org]
comment: This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.
is_a: EDAM_data:1190 ! Tool name

[Term]
id: EDAM_data:1194
name: Tool name (EMBOSS)
namespace: identifier
subset: identifiers
subset: data
def: "The name of an EMBOSS application." [http://edamontology.org]
is_a: EDAM_data:1190 ! Tool name

[Term]
id: EDAM_data:1195
name: Tool name (EMBASSY package)
namespace: identifier
subset: identifiers
subset: data
def: "The name of an EMBASSY package." [http://edamontology.org]
is_a: EDAM_data:1190 ! Tool name


[Term]
id: EDAM_data:2098
name: Job identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a submitted job." [http://edamontology.org]
synonym: "Computation ID" EXACT [http://wsio.org/data_009]
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:1676
name: Job ID
namespace: identifier
subset: identifiers
subset: data
def: "The (typically numeric) unique identifier of a submitted job." [http://edamontology.org]
! is_a: EDAM_data:2098 ! Job identifier
is_obsolete: true !{since=1.0}
replaced_by: EDAM_data:2098 ! Job identifier


[Term]
id: EDAM_data:2118
name: Person identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a software end-user (typically a person)." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:2101
name: User ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a software end-user (typically a person)." [http://edamontology.org]
is_a: EDAM_data:2118 ! Person identifier


[Term]
id: EDAM_data:1689
name: Username
namespace: identifier
subset: identifiers
subset: data
def: "A username on a computer system." [http://edamontology.org]
is_a: EDAM_data:2101 ! User ID


[Term]
id: EDAM_data:1690
name: Password
namespace: identifier
subset: identifiers
subset: data
def: "A password on a computer system." [http://edamontology.org]
is_a: EDAM_data:2101 ! User ID


[Term]
id: EDAM_data:1691
name: Email address
namespace: identifier
subset: identifiers
subset: data
def: "A valid email address of an end-user." [http://edamontology.org]
xref: Moby:Email
xref: Moby:EmailAddress
is_a: EDAM_data:2101 ! User ID


[Term]
id: EDAM_data:1692
name: Person name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a person." [http://edamontology.org]
is_a: EDAM_data:2118 ! Person identifier


[Term]
id: EDAM_data:1881
name: Author ID
namespace: identifier
subset: identifiers
subset: data
def: "Information on the authors of a published work." [http://edamontology.org]
xref: Moby:Author
is_a: EDAM_data:2118 ! Person identifier

[Term]
id: EDAM_data:1882
name: DragonDB author identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier representing an author in the DragonDB database." [http://edamontology.org]
is_a: EDAM_data:1881 ! Author ID




[Term]
id: EDAM_data:2596
name: Catalogue identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a catalogue of biological resources." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:2779
name: Stock number
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:3022
name: NCBI genetic code ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a genetic code in the NCBI list of genetic codes." [http://edamontology.org]
regex: "[1-9][0-9]?"
example: "16"
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:0982
name: Molecule identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a molecule." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2529 ! Molecule report

[Term]
id: EDAM_data:1015
name: Sequence feature ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:3034 ! Sequence feature identifier

[Term]
id: EDAM_data:3107 {since=beta13}
name: Sequence feature name
namespace: identifier
subset: identifiers
subset: data
def: "A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name
is_a: EDAM_data:3034 ! Sequence feature identifier




[Term]
id: EDAM_data:3034 {since=beta13}
name: Sequence feature identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2914 ! Sequence features metadata
relationship: is_identifier_of EDAM_data:1255 ! Feature record

[Term]
id: EDAM_data:1023
name: EMBOSS Uniform Feature Object
namespace: data
subset: data
def: "The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications." [http://edamontology.org]
synonym: "UFO" EXACT [http://edamontology.org]
is_a: EDAM_data:3034 ! Sequence feature identifier
is_a: EDAM_data:2099 ! Name




[Term]
id: EDAM_data:1893
name: Locus ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org]
synonym: "Locus name" EXACT [http://edamontology.org]
synonym: "Locus identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:2012 ! Map position


[Term]
id: EDAM_data:2340
name: Genome build identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a build of a particular genome." [http://edamontology.org]
is_a: EDAM_data:2749 ! Genome identifier

[Term]
id: EDAM_data:2749
name: Genome identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a particular genome." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:2903
name: Genome accession
namespace: identifier
subset: identifiers
subset: data
def: "An accession of a particular genome (in a database)." [http://edamontology.org]
is_a: EDAM_data:2749 ! Genome identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1025
name: Gene identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [http://edamontology.org]
xref: Moby:GeneAccessionList
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0916 ! Gene annotation


[Term]
id: EDAM_data:2795
name: ORF identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an open reading frame." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:2727
name: Promoter ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a promoter of a gene that is catalogued in a database." [http://edamontology.org]
xref: Moby:GeneAccessionList
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2630
name: Mobile genetic element ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a mobile genetic element." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2127
name: Genetic code identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a genetic code." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1598 ! Genetic code

[Term]
id: EDAM_data:1038
name: Protein domain ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein structural domain." [http://edamontology.org]
comment: This is typically a character or string concatenated with a PDB identifier and a chain identifier.
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:1468 ! Protein domain

[Term]
id: EDAM_data:2618
name: Protein modification ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein modification catalogued in a database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1867
name: Protein fold name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a protein fold." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:2655
name: Cell type identifier
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a type or group of cells." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:2893
name: Cell type accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a type or group of cells (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:2655 ! Cell type identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1869
name: Organism identifier
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a (group of) organisms." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2530 ! Organism annotation

[Term]
id: EDAM_data:2908
name: Organism accession
namespace: identifier
subset: identifiers
subset: data
def: "An accession of annotation on a (group of) organisms (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:1869 ! Organism identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2909
name: Organism name
namespace: identifier
subset: identifiers
subset: data
def: "The name of an organism (or group of organisms)." [http://edamontology.org]
xref: Moby:Organism_Name
xref: Moby:OrganismsLongName
xref: Moby:OrganismsShortName
xref: Moby:FirstEpithet
xref: Moby:InfraspecificEpithet
xref: Moby:OccurrenceRecord
xref: Moby:BriefOccurrenceRecord
is_a: EDAM_data:1869 ! Organism identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:1048
name: Database identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a biological or bioinformatics database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0957 ! Database metadata

[Term]
id: EDAM_data:1049
name: Directory name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a directory." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name
is_a: EDAM_data:0583 ! Directory metadata

[Term]
id: EDAM_data:1050
name: File name
namespace: identifier
subset: identifiers
subset: data
def: "The name (or part of a name) of a file (of any type)." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:1051
name: Ontology name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name
is_a: EDAM_data:2338 ! Ontology identifier
relationship: is_identifier_of EDAM_data:0582 ! Ontology

[Term]
id: EDAM_data:2110
name: Molecular property identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a molecular property." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2087 ! Molecular property


[Term]
id: EDAM_data:1062
name: Database entry identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type." [http://edamontology.org]
comment: This concept is required for completeness. It should never have child concepts.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier


[Term]
id: EDAM_data:2117
name: Map identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a map of a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1274 ! Map

[Term]
id: EDAM_data:2904
name: Map accession
namespace: identifier
subset: identifiers
subset: data
def: "An accession of a map of a molecular sequence (deposited in a database)." [http://edamontology.org]
is_a: EDAM_data:2117 ! Map identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1063
name: Sequence identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of molecular sequence(s) or entries from a molecular sequence database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:0855 ! Sequence metadata
relationship: is_identifier_of EDAM_data:2044 ! Sequence


[Term]
id: EDAM_data:2294
name: Sequence variation ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an entry from a database of molecular sequence variation." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1064
name: Sequence set ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a set of molecular sequence(s)." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0850 ! Sequence set

[Term]
id: EDAM_data:1065
name: Sequence signature identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1114 ! Sequence motif identifier
consider: EDAM_data:1115 ! Sequence profile ID

[Term]
id: EDAM_data:1066
name: Sequence alignment ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a molecular sequence alignment, for example a record from an alignment database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_data:1067
name: Phylogenetic distance matrix identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a phylogenetic distance matrix." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:1068
name: Phylogenetic tree ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a phylogenetic tree for example from a phylogenetic tree database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0872 ! Phylogenetic tree


[Term]
id: EDAM_data:3036 {since=beta13}
name: Matrix identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an array of numerical values, such as a comparison matrix." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2082 ! Matrix


[Term]
id: EDAM_data:1069
name: Comparison matrix identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a comparison matrix." [http://edamontology.org]
synonym: "Substitution matrix identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:3036 ! Matrix identifier
relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix


[Term]
id: EDAM_data:3035 {since=beta13}
name: Structure identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0883 ! Structure

[Term]
id: EDAM_data:1070
name: Structure ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database." [http://edamontology.org]
is_a: EDAM_data:3035 ! Structure identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1759
name: PDB model number
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a model structure from a PDB file." [http://edamontology.org]
synonym: "Model number" EXACT [http://edamontology.org]
xref: WHATIF: model_number
is_a: EDAM_data:3035 ! Structure identifier
! pdbx_PDB_model_num in PDBML


[Term]
id: EDAM_data:1071
name: Structural (3D) profile ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment)." [http://edamontology.org]
synonym: "Structural profile identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0889 ! Structural (3D) profile

[Term]
id: EDAM_data:1072
name: Structure alignment ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of tertiary structure alignments." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0886 ! Structure alignment

[Term]
id: EDAM_data:1073
name: Amino acid index ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an index of amino acid physicochemical and biochemical property data." [http://edamontology.org]
is_a: EDAM_data:3036 ! Matrix identifier
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:1501 ! Amino acid index


[Term]
id: EDAM_data:2627
name: Molecular interaction ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a report of molecular interactions from a database (typically)." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:2599 ! Molecular interaction

[Term]
id: EDAM_data:1075
name: Protein family identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein family." [http://edamontology.org]
synonym: "Protein secondary database record identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0907 ! Protein family

[Term]
id: EDAM_data:2910
name: Protein family accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a protein family (that is deposited in a database)." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:1075 ! Protein family identifier

[Term]
id: EDAM_data:1131
name: Protein family name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a protein family." [http://edamontology.org]
is_a: EDAM_data:1075 ! Protein family identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2355
name: RNA family identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an RNA family, typically an entry from a RNA sequence classification database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2354 ! RNA family annotation


[Term]
id: EDAM_data:2111
name: Codon usage table identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a codon usage table, for example a genetic code." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1597 ! Codon usage table
relationship: is_identifier_of EDAM_data:1598 ! Genetic code


[Term]
id: EDAM_data:1077
name: Transcription factor identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a transcription factor (or a TF binding site)." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:0989 ! Protein identifier
relationship: is_identifier_of EDAM_data:1315 ! Gene features (TFBS)

[Term]
id: EDAM_data:2911
name: Transcription factor accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of an entry from a database of transcription factors or binding sites." [http://edamontology.org]
is_a: EDAM_data:1077 ! Transcription factor identifier
is_a: EDAM_data:2907 ! Protein accession
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1078
name: Microarray experiment annotation ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of microarray data." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray)

[Term]
id: EDAM_data:1079
name: Electron microscopy model ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of electron microscopy data." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0941 ! Electron microscopy model


[Term]
id: EDAM_data:1080
name: Gene expression report ID
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:2708
def: "Accession of a report of gene expression (e.g. a gene expression profile) from a database." [http://edamontology.org]
synonym: "Gene expression profile identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:3111 ! Processed microarray data

[Term]
id: EDAM_data:1081
name: Genotype and phenotype annotation ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation


[Term]
id: EDAM_data:2382
name: Genotype experiment ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of genotype experiment metadata." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:2381 ! Experiment annotation (genotype)

[Term]
id: EDAM_data:2638
name: PubChem bioassay ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an assay from the PubChem database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2639 ! PubChem identifier

[Term]
id: EDAM_data:1082
name: Pathway or network identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of biological pathways or networks." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2600 ! Pathway or network

[Term]
id: EDAM_data:2590
name: Hierarchy identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of biological hierarchies." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2891 ! Biological model accession

[Term]
id: EDAM_data:2108
name: Reaction ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological reaction from a database." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2978 ! Reaction data


[Term]
id: EDAM_data:1083
name: Workflow ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological or biomedical workflow, typically from a database of workflows." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:2972 ! Workflow

[Term]
id: EDAM_data:1084
name: Data resource definition identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a data type definition from some provider." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:2219
name: Database field name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a field in a database." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:1085
name: Biological model identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a mathematical model, typically an entry from a database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0950 ! Biological model

[Term]
id: EDAM_data:2891
name: Biological model accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a mathematical model, typically an entry from a database." [http://edamontology.org]
is_a: EDAM_data:1085 ! Biological model identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1086
name: Compound identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of chemicals." [http://edamontology.org]
synonym: "Small molecule identifier" EXACT [http://edamontology.org]
synonym: "Chemical compound identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
relationship: is_identifier_of EDAM_data:0962 ! Small molecule annotation
relationship: is_identifier_of EDAM_data:1712 ! Structure image (small molecule)
relationship: is_identifier_of EDAM_data:0846 ! Chemical formula

[Term]
id: EDAM_data:2894
name: Compound accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of an entry from a database of chemicals." [http://edamontology.org]
synonym: "Small molecule accession" EXACT [http://edamontology.org]
synonym: "Chemical compound accession" EXACT [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
is_a: EDAM_data:2901 ! Molecule accession

[Term]
id: EDAM_data:2338
name: Ontology identifier
namespace: identifier
subset: identifiers
subset: data
def: "Any arbitrary identifier of an ontology." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0582 ! Ontology


[Term]
id: EDAM_data:3025
name: Ontology concept identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:2858 ! Ontology concept

[Term]
id: EDAM_data:1087
name: Ontology concept ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations." [http://edamontology.org]
synonym: "Ontology concept ID" EXACT [http://edamontology.org]
is_a: EDAM_data:3025 ! Ontology concept identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1088
name: Article ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a scientific article." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:0971 ! Article

[Term]
id: EDAM_data:2633
name: Book ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a book." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:2790
name: Gel identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a two-dimensional (protein) gel." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:2791
name: Reference map name (SWISS-2DPAGE)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a reference map gel from the SWISS-2DPAGE database." [http://edamontology.org]
is_a: EDAM_data:2790 ! Gel identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2373
name: Spot ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a spot from a two-dimensional (protein) gel." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2587
name: Blot ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a blot from a Northern Blot." [http://edamontology.org]
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:0976 ! Identifier (typed)

[Term]
id: EDAM_data:2379
name: Strain identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org]
is_a: EDAM_data:1869 ! Organism identifier

[Term]
id: EDAM_data:2912
name: Strain accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org]
is_a: EDAM_data:2379 ! Strain identifier
is_a: EDAM_data:2908 ! Organism accession
relationship: is_identifier_of EDAM_data:0963 ! Cell line annotation


[Term]
id: EDAM_data:2917
name: ConsensusPathDB identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an entity from the ConsensusPathDB database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)


[Term]
id: EDAM_data:2776
name: ConsensusPathDB entity ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a physical entity from the ConsensusPathDB database." [http://edamontology.org]
is_a: EDAM_data:2917 ! ConsensusPathDB identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2777
name: ConsensusPathDB entity name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a physical entity from the ConsensusPathDB database." [http://edamontology.org]
is_a: EDAM_data:2917 ! ConsensusPathDB identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2639
name: PubChem identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the PubChem database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2367
name: ASTD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an object from the ASTD database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1089
name: FlyBase ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an object from the FlyBase database." [http://edamontology.org]
regex: "FB[a-zA-Z_0-9]{2}[0-9]{7}"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2113
name: WormBase identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an object from the WormBase database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)

[Term]
id: EDAM_data:2104
name: BioCyc ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an object from one of the BioCyc databases." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:1154
name: KEGG object identifier
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an object from one of the KEGG databases (excluding the GENES division)." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2380
name: CABRI accession
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of an item from the CABRI database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2387
name: TAIR accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the TAIR database." [http://edamontology.org]
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2610
name: Ensembl ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database." [http://edamontology.org]
regex: "ENS[A-Z]*[FPTG][0-9]{11}"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2620
name: RGD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the RGD database." [http://edamontology.org]
regex: "[0-9]{4,7}"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2632
name: SGD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the Saccharomyces genome database (SGD)." [http://edamontology.org]
regex: "PWY[a-zA-Z_0-9]{2}\-[0-9]{3}"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2649
name: PharmGKB ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org]
regex: "PA[0-9]+"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2368
name: ASTD ID (exon)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an exon from the ASTD database." [http://edamontology.org]
is_a: EDAM_data:2367 ! ASTD ID


[Term]
id: EDAM_data:2369
name: ASTD ID (intron)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an intron from the ASTD database." [http://edamontology.org]
is_a: EDAM_data:2367 ! ASTD ID


[Term]
id: EDAM_data:2370
name: ASTD ID (polya)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a polyA signal from the ASTD database." [http://edamontology.org]
is_a: EDAM_data:2367 ! ASTD ID


[Term]
id: EDAM_data:2371
name: ASTD ID (tss)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a transcription start site from the ASTD database." [http://edamontology.org]
is_a: EDAM_data:2367 ! ASTD ID

[Term]
id: EDAM_data:2671
name: Ensembl ID (Homo sapiens)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division)." [http://edamontology.org]
regex: "ENS([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2672
name: Ensembl ID ('Bos taurus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org]
regex: "ENSBTA([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2673
name: Ensembl ID ('Canis familiaris')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org]
regex: "ENSCAF([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2674
name: Ensembl ID ('Cavia porcellus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org]
regex: "ENSCPO([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2675
name: Ensembl ID ('Ciona intestinalis')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org]
regex: "ENSCIN([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2676
name: Ensembl ID ('Ciona savignyi')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org]
regex: "ENSCSAV([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2677
name: Ensembl ID ('Danio rerio')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." [http://edamontology.org]
regex: "ENSDAR([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2678
name: Ensembl ID ('Dasypus novemcinctus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." [http://edamontology.org]
regex: "ENSDNO([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2679
name: Ensembl ID ('Echinops telfairi')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." [http://edamontology.org]
regex: "ENSETE([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2680
name: Ensembl ID ('Erinaceus europaeus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." [http://edamontology.org]
regex: "ENSEEU([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2681
name: Ensembl ID ('Felis catus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." [http://edamontology.org]
regex: "ENSFCA([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2682
name: Ensembl ID ('Gallus gallus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." [http://edamontology.org]
regex: "ENSGAL([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2683
name: Ensembl ID ('Gasterosteus aculeatus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." [http://edamontology.org]
regex: "ENSGAC([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2684
name: Ensembl ID ('Homo sapiens')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." [http://edamontology.org]
regex: "ENSHUM([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2685
name: Ensembl ID ('Loxodonta africana')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." [http://edamontology.org]
regex: "ENSLAF([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2686
name: Ensembl ID ('Macaca mulatta')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." [http://edamontology.org]
regex: "ENSMMU([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2687
name: Ensembl ID ('Monodelphis domestica')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." [http://edamontology.org]
regex: "ENSMOD([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2688
name: Ensembl ID ('Mus musculus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." [http://edamontology.org]
regex: "ENSMUS([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2689
name: Ensembl ID ('Myotis lucifugus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." [http://edamontology.org]
regex: "ENSMLU([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2690
name: Ensembl ID ("Ornithorhynchus anatinus")
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." [http://edamontology.org]
regex: "ENSOAN([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2691
name: Ensembl ID ('Oryctolagus cuniculus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." [http://edamontology.org]
regex: "ENSOCU([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2692
name: Ensembl ID ('Oryzias latipes')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." [http://edamontology.org]
regex: "ENSORL([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2693
name: Ensembl ID ('Otolemur garnettii')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." [http://edamontology.org]
regex: "ENSSAR([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2694
name: Ensembl ID ('Pan troglodytes')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." [http://edamontology.org]
regex: "ENSPTR([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2695
name: Ensembl ID ('Rattus norvegicus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org]
regex: "ENSRNO([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2696
name: Ensembl ID ('Spermophilus tridecemlineatus')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org]
regex: "ENSSTO([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2697
name: Ensembl ID ('Takifugu rubripes')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." [http://edamontology.org]
regex: "ENSFRU([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2698
name: Ensembl ID ('Tupaia belangeri')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." [http://edamontology.org]
regex: "ENSTBE([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2699
name: Ensembl ID ('Xenopus tropicalis')
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." [http://edamontology.org]
regex: "ENSXET([EGTP])[0-9]{11}"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2610 ! Ensembl ID

[Term]
id: EDAM_data:2725
name: Transcript ID (Ensembl)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a gene transcript from the Ensembl database." [http://edamontology.org]
synonym: "Ensembl Transcript ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2610 ! Ensembl ID
is_a: EDAM_data:2769 ! Transcript ID


[Term]
id: EDAM_data:2597
name: CABRI catalogue name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a catalogue of biological resources from the CABRI database." [http://edamontology.org]
is_a: EDAM_data:2596 ! Catalogue identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2780
name: Stock number (TAIR)
namespace: identifier
subset: identifiers
subset: data
def: "A stock number from The Arabidopsis information resource (TAIR)." [http://edamontology.org]
is_a: EDAM_data:2779 ! Stock number

[Term]
id: EDAM_data:2129
name: File format name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2131
name: Operating system name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a computer operating system such as Linux, PC or Mac." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:2538
name: Mutation identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a mutation." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:2209
name: Mutation ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a specific mutation catalogued in a database." [http://edamontology.org]
is_a: EDAM_data:2538 ! Mutation identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2133
name: Logical operator
namespace: identifier
subset: identifiers
subset: data
def: "A logical operator such as OR, AND, XOR, and NOT." [http://edamontology.org]
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:1114
name: Sequence motif identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a sequence motif, for example an entry from a motif database." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
relationship: is_identifier_of EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_data:1115
name: Sequence profile ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a sequence profile." [http://edamontology.org]
comment: A sequence profile typically represents a sequence alignment.
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:1354 ! Sequence profile


[Term]
id: EDAM_data:2660
name: BioNumbers ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:0983
name: Atom identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier (e.g. character symbol) of a specific atom." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)


[Term]
id: EDAM_data:0984
name: Molecule name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a specific molecule." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:2901
name: Molecule accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a specific molecule (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:0986
name: Chemical identifier
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a chemical compound." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1086 ! Compound identifier


[Term]
id: EDAM_data:2119
name: Nucleic acid identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a nucleic acid molecule." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
relationship: is_identifier_of EDAM_data:2084 ! Nucleic acid report


[Term]
id: EDAM_data:0988
name: Peptide identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a peptide chain." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier

[Term]
id: EDAM_data:2906
name: Peptide ID
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a peptide deposited in a database." [http://edamontology.org]
is_a: EDAM_data:0988 ! Peptide identifier
is_a: EDAM_data:2901 ! Molecule accession

[Term]
id: EDAM_data:1008
name: Polypeptide chain ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a polypeptide chain from a protein." [http://edamontology.org]
comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
synonym: "Polypeptide chain identifier" EXACT [http://edamontology.org]
synonym: "Protein chain identifier" EXACT [http://edamontology.org]
synonym: "PDB chain identifier" EXACT [http://edamontology.org]
synonym: "Chain identifier" EXACT [http://edamontology.org]
synonym: "PDB strand id" EXACT [http://edamontology.org]
xref: WHATIF: chain
is_a: EDAM_data:0988 ! Peptide identifier
relationship: is_identifier_of EDAM_data:1467 ! Protein chain
! pdbx_PDB_strand_id in PDBML

[Term]
id: EDAM_data:0989
name: Protein identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
relationship: is_identifier_of EDAM_data:0896 ! Protein report

[Term]
id: EDAM_data:2907
name: Protein accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a protein deposited in a database." [http://edamontology.org]
is_a: EDAM_data:0989 ! Protein identifier
is_a: EDAM_data:2901 ! Molecule accession

[Term]
id: EDAM_data:1757
name: Atom name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an atom." [http://edamontology.org]
is_a: EDAM_data:0983 ! Atom identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:1748
name: PDB atom name
namespace: identifier
subset: identifiers
subset: data
def: "Identifier (a string) of a specific atom from a PDB file for a molecular structure." [http://edamontology.org]
xref: WHATIF: atom_type
xref: WHATIF: alternate_atom
xref: WHATIF: PDBx_auth_atom_id
xref: WHATIF: PDBx_type_symbol
is_a: EDAM_data:1757 ! Atom name
! pdbx_PDB_atom_name in PDBML

[Term]
id: EDAM_data:0990
name: Compound name
namespace: identifier
subset: identifiers
subset: data
def: "Unique name of a chemical compound." [http://edamontology.org]
synonym: "Chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
is_a: EDAM_data:0984 ! Molecule name

[Term]
id: EDAM_data:0991
name: Chemical registry number
namespace: identifier
subset: identifiers
subset: data
def: "Unique registry number of a chemical compound." [http://edamontology.org]
is_a: EDAM_data:2894 ! Compound accession


[Term]
id: EDAM_data:0992
name: Ligand identifier
namespace: identifier
subset: identifiers
subset: data
def: "Code word for a ligand, for example from a PDB file." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1086 ! Compound identifier

[Term]
id: EDAM_data:0993
name: Drug identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a drug." [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
relationship: is_identifier_of EDAM_data:2851 ! Drug structure


[Term]
id: EDAM_data:2895
name: Drug accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a drug." [http://edamontology.org]
is_a: EDAM_data:0993 ! Drug identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2899
name: Drug name
namespace: identifier
subset: identifiers
subset: data
def: "Common name of a drug." [http://edamontology.org]
is_a: EDAM_data:0993 ! Drug identifier
is_a: EDAM_data:0990 ! Compound name


[Term]
id: EDAM_data:2576
name: Toxin identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a toxin." [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
relationship: is_identifier_of EDAM_data:2852 ! Toxin structure

[Term]
id: EDAM_data:2896
name: Toxin name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a toxin." [http://edamontology.org]
is_a: EDAM_data:2576 ! Toxin identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2897
name: Toxin accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a toxin (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:2576 ! Toxin identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:0994
name: Amino acid identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an amino acid." [http://edamontology.org]
synonym: "Residue identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
relationship: is_identifier_of EDAM_data:2016 ! Amino acid property


[Term]
id: EDAM_data:0995
name: Nucleotide identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a nucleotide." [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier

[Term]
id: EDAM_data:0996
name: Monosaccharide identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a monosaccharide." [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier


[Term]
id: EDAM_data:2898
name: Monosaccharide accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a monosaccharide (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:0996 ! Monosaccharide identifier
is_a: EDAM_data:2091 ! Accession

[Term]
id: EDAM_data:2812
name: Lipid identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a lipid." [http://edamontology.org]
is_a: EDAM_data:0982 ! Molecule identifier
relationship: is_identifier_of EDAM_data:2850 ! Lipid structure
relationship: is_identifier_of EDAM_data:2879 ! Lipid structure report


[Term]
id: EDAM_data:2905
name: Lipid accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of an entry from a database of lipids." [http://edamontology.org]
is_a: EDAM_data:2812 ! Lipid identifier
is_a: EDAM_data:2901 ! Molecule accession

[Term]
id: EDAM_data:2663
name: Carbohydrate identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a carbohydrate." [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier
relationship: is_identifier_of EDAM_data:2313 ! Carbohydrate structure report
relationship: is_identifier_of EDAM_data:1462 ! Carbohydrate structure


[Term]
id: EDAM_data:2900
name: Carbohydrate accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of an entry from a database of carbohydrates." [http://edamontology.org]
is_a: EDAM_data:2663 ! Carbohydrate identifier
is_a: EDAM_data:2901 ! Molecule accession


[Term]
id: EDAM_data:2605
name: Compound ID (KEGG)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a chemical compound from the KEGG database." [http://edamontology.org]
synonym: "KEGG compound ID" EXACT [http://edamontology.org]
synonym: "KEGG compound identifier" EXACT [http://edamontology.org]
regex: "C[0-9]+"
is_a: EDAM_data:2894 ! Compound accession
is_a: EDAM_data:1154 ! KEGG object identifier

[Term]
id: EDAM_data:2580
name: BindingDB Monomer ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a monomer from the BindingDB database." [http://edamontology.org]
is_a: EDAM_data:2894 ! Compound accession


[Term]
id: EDAM_data:1172
name: PubChem CID
namespace: identifier
subset: identifiers
subset: data
def: "Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure." [http://edamontology.org]
synonym: "PubChem compound accession identifier" EXACT [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2894 ! Compound accession
is_a: EDAM_data:2639 ! PubChem identifier

[Term]
id: EDAM_data:1173
name: ChemSpider ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the ChemSpider database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:1174
name: ChEBI ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the ChEBI database." [http://edamontology.org]
synonym: "ChEBI identifier" EXACT [http://edamontology.org]
regex: "CHEBI:[0-9]+"
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:2105
name: Compound ID (BioCyc)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a compound from the BioCyc chemical compounds database." [http://edamontology.org]
synonym: "BioCyc compound ID" EXACT [http://edamontology.org]
synonym: "BioCyc compound identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2104 ! BioCyc ID
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:2622
name: Compound ID (HMDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB)." [http://edamontology.org]
synonym: "HMDB ID" EXACT [http://edamontology.org]
regex: "HMDB[0-9]{5}"
is_a: EDAM_data:2894 ! Compound accession


[Term]
id: EDAM_data:2635
name: Compound ID (3DMET)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a metabolite from the 3DMET database." [http://edamontology.org]
synonym: "3DMET ID" EXACT [http://edamontology.org]
regex: "B[0-9]{5}"
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:2646
name: Compound ID (ChEMBL)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a small molecular from the ChEMBL database." [http://edamontology.org]
synonym: "ChEMBL ID" EXACT [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:2658
name: Compound ID (ChemIDplus)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a chemical from the ChemIDplus database." [http://edamontology.org]
synonym: "ChemIDplus ID" EXACT [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2894 ! Compound accession

[Term]
id: EDAM_data:0997
name: Chemical name (ChEBI)
namespace: identifier
subset: identifiers
subset: data
def: "Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound." [http://edamontology.org]
comment: This is the recommended chemical name for use for example in database annotation.
synonym: "ChEBI chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:0998
name: Chemical name (IUPAC)
namespace: identifier
subset: identifiers
subset: data
def: "IUPAC recommended name of a chemical compound." [http://edamontology.org]
synonym: "IUPAC chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:0999
name: Chemical name (INN)
namespace: identifier
subset: identifiers
subset: data
def: "International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO)." [http://edamontology.org]
synonym: "INN chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:1000
name: Chemical name (brand)
namespace: identifier
subset: identifiers
subset: data
def: "Brand name of a chemical compound." [http://edamontology.org]
synonym: "Brand chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:1001
name: Chemical name (synonymous)
namespace: identifier
subset: identifiers
subset: data
def: "Synonymous name of a chemical compound." [http://edamontology.org]
synonym: "Synonymous chemical name" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:1002
name: Chemical registry number (CAS)
namespace: identifier
subset: identifiers
subset: data
def: "CAS registry number of a chemical compound." [http://edamontology.org]
synonym: "CAS chemical registry number" EXACT [http://edamontology.org]
is_a: EDAM_data:0991 ! Chemical registry number

[Term]
id: EDAM_data:1003
name: Chemical registry number (Beilstein)
namespace: identifier
subset: identifiers
subset: data
def: "Beilstein registry number of a chemical compound." [http://edamontology.org]
synonym: "Beilstein chemical registry number" EXACT [http://edamontology.org]
is_a: EDAM_data:0991 ! Chemical registry number

[Term]
id: EDAM_data:1004
name: Chemical registry number (Gmelin)
namespace: identifier
subset: identifiers
subset: data
def: "Gmelin registry number of a chemical compound." [http://edamontology.org]
synonym: "Gmelin chemical registry number" EXACT [http://edamontology.org]
is_a: EDAM_data:0991 ! Chemical registry number

[Term]
id: EDAM_data:1005
name: HET group name
namespace: identifier
subset: identifiers
subset: data
def: "3-letter code word for a ligand (HET group) from a PDB file, for example ATP." [http://edamontology.org]
synonym: "Short ligand name" EXACT [http://edamontology.org]
synonym: "Component identifier code" EXACT [http://edamontology.org]
is_a: EDAM_data:0990 ! Compound name


[Term]
id: EDAM_data:2613
name: KEGG Glycan ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND)." [http://edamontology.org]
regex: "G[0-9]+"
is_a: EDAM_data:2900 ! Carbohydrate accession
is_a: EDAM_data:1154 ! KEGG object identifier


[Term]
id: EDAM_data:2326
name: DrugBank ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a drug from the DrugBank database." [http://edamontology.org]
regex: "DB[0-9]{5}"
is_a: EDAM_data:2895 ! Drug accession

[Term]
id: EDAM_data:2609
name: Drug ID (KEGG)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a drug from the KEGG Drug database." [http://edamontology.org]
regex: "D[0-9]+"
is_a: EDAM_data:2895 ! Drug accession
is_a: EDAM_data:1154 ! KEGG object identifier

[Term]
id: EDAM_data:2652
name: Drug ID (PharmGKB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org]
regex: "PA[0-9]+"
is_a: EDAM_data:2895 ! Drug accession
is_a: EDAM_data:2649 ! PharmGKB ID


[Term]
id: EDAM_data:2653
name: Drug ID (TTD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a drug from the Therapeutic Target Database (TTD)." [http://edamontology.org]
regex: "DAP[0-9]+"
is_a: EDAM_data:2895 ! Drug accession

[Term]
id: EDAM_data:3102 {since=beta13}
name: CAS number
namespace: identifier
subset: identifiers
subset: data
def: "Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service." [http://edamontology.org]
synonym: "CAS registry number" EXACT [http://edamontology.org]
is_a: EDAM_data:2895 ! Drug accession

[Term]
id: EDAM_data:3103 {since=beta13}
name: ATC code
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC)." [http://edamontology.org]
is_a: EDAM_data:2895 ! Drug accession

[Term]
id: EDAM_data:3104 {since=beta13}
name: UNII
namespace: identifier
subset: identifiers
subset: data
def: "A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA)." [http://edamontology.org]
synonym: "Unique Ingredient Identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1086 ! Compound identifier





[Term]
id: EDAM_data:2578
name: ArachnoServer ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a toxin from the ArachnoServer database." [http://edamontology.org]
is_a: EDAM_data:2897 ! Toxin accession


[Term]
id: EDAM_data:2662
name: T3DB ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database." [http://edamontology.org]
regex: "T3D[0-9]+"
is_a: EDAM_data:2897 ! Toxin accession

[Term]
id: EDAM_data:1006
name: Amino acid name
namespace: identifier
subset: identifiers
subset: data
def: "String of one or more ASCII characters representing an amino acid." [http://edamontology.org]
is_a: EDAM_data:0994 ! Amino acid identifier

[Term]
id: EDAM_data:2563
name: Amino acid name (single letter)
namespace: identifier
subset: identifiers
subset: data
def: "Single letter amino acid identifier, e.g. G." [http://edamontology.org]
is_a: EDAM_data:1006 ! Amino acid name

[Term]
id: EDAM_data:2564
name: Amino acid name (three letter)
namespace: identifier
subset: identifiers
subset: data
def: "Three letter amino acid identifier, e.g. GLY." [http://edamontology.org]
is_a: EDAM_data:1006 ! Amino acid name


[Term]
id: EDAM_data:1758
name: PDB residue name
namespace: identifier
subset: identifiers
subset: data
def: "Three-letter amino acid residue names as used in PDB files." [http://edamontology.org]
xref: WHATIF: type
is_a: EDAM_data:2564 ! Amino acid name (three letter)



[Term]
id: EDAM_data:2565
name: Amino acid name (full name)
namespace: identifier
subset: identifiers
subset: data
def: "Full name of an amino acid, e.g. Glycine." [http://edamontology.org]
is_a: EDAM_data:1006 ! Amino acid name


[Term]
id: EDAM_data:1007
name: Nucleotide code
namespace: identifier
subset: identifiers
subset: data
def: "String of one or more ASCII characters representing a nucleotide." [http://edamontology.org]
is_a: EDAM_data:0995 ! Nucleotide identifier
is_a: EDAM_data:0990 ! Compound name

[Term]
id: EDAM_data:2746
name: MonosaccharideDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a monosaccharide from the MonosaccharideDB database." [http://edamontology.org]
is_a: EDAM_data:2898 ! Monosaccharide accession

[Term]
id: EDAM_data:2625
name: LIPID MAPS ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the LIPID MAPS database." [http://edamontology.org]
synonym: "LM ID" EXACT [http://edamontology.org]
regex: "LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})?"
is_a: EDAM_data:2905 ! Lipid accession


[Term]
id: EDAM_data:2665
name: LipidBank ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the LipidBank database." [http://edamontology.org]
regex: "[a-zA-Z_0-9]+[0-9]+"
is_a: EDAM_data:2905 ! Lipid accession


[Term]
id: EDAM_data:2664
name: GlycomeDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the GlycomeDB database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2900 ! Carbohydrate accession


[Term]
id: EDAM_data:2752
name: GlycoMap ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2900 ! Carbohydrate accession

[Term]
id: EDAM_data:2796
name: Linucs ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the GlycosciencesDB database." [http://edamontology.org]
is_a: EDAM_data:2900 ! Carbohydrate accession


[Term]
id: EDAM_data:0987
name: Chromosome name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a chromosome." [http://edamontology.org]
is_a: EDAM_data:2119 ! Nucleic acid identifier
is_a: EDAM_data:0984 ! Molecule name
relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome)

[Term]
id: EDAM_data:2208
name: Plasmid identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a plasmid in a database." [http://edamontology.org]
is_a: EDAM_data:2119 ! Nucleic acid identifier

[Term]
id: EDAM_data:2718
name: Oligonucleotide ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an oligonucleotide from a database." [http://edamontology.org]
is_a: EDAM_data:2119 ! Nucleic acid identifier
is_a: EDAM_data:2901 ! Molecule accession


[Term]
id: EDAM_data:2769
name: Transcript ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a RNA transcript." [http://edamontology.org]
is_a: EDAM_data:2119 ! Nucleic acid identifier
is_a: EDAM_data:2901 ! Molecule accession
relationship: is_identifier_of EDAM_data:2399 ! Gene annotation (transcript)

[Term]
id: EDAM_data:2706
name: Chromosome name (BioCyc)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a chromosome as used in the BioCyc database." [http://edamontology.org]
is_a: EDAM_data:0987 ! Chromosome name


[Term]
id: EDAM_data:2719
name: dbProbe ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an oligonucleotide probe from the dbProbe database." [http://edamontology.org]
is_a: EDAM_data:2718 ! Oligonucleotide ID

[Term]
id: EDAM_data:2721
name: DiProDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an dinucleotide property from the DiProDB database." [http://edamontology.org]
is_a: EDAM_data:2718 ! Oligonucleotide ID

[Term]
id: EDAM_data:2770
name: HIT ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an RNA transcript from the H-InvDB database." [http://edamontology.org]
is_a: EDAM_data:2769 ! Transcript ID


[Term]
id: EDAM_data:2626
name: PeptideAtlas ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a peptide from the PeptideAtlas peptide databases." [http://edamontology.org]
regex: "PAp[0-9]{8}"
is_a: EDAM_data:2906 ! Peptide ID
! pdbx_PDB_strand_id in PDBML

[Term]
id: EDAM_data:1009
name: Protein name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a protein." [http://edamontology.org]
is_a: EDAM_data:0989 ! Protein identifier
is_a: EDAM_data:0984 ! Molecule name

[Term]
id: EDAM_data:1010
name: Enzyme identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of an enzyme or record from a database of enzymes." [http://edamontology.org]
is_a: EDAM_data:0989 ! Protein identifier
relationship: is_identifier_of EDAM_data:1509 ! Enzyme property


[Term]
id: EDAM_data:2114
name: WormBase wormpep ID
namespace: identifier
subset: identifiers
subset: data
def: "Protein identifier used by WormBase database." [http://edamontology.org]
regex: "CE[0-9]{5}"
is_a: EDAM_data:2907 ! Protein accession
is_a: EDAM_data:2113 ! WormBase identifier

[Term]
id: EDAM_data:2804
name: Protein ID (ConoServer)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a cone snail toxin protein from the ConoServer database." [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2802
name: Protein ID (EcID)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a protein from the EcID database." [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:3029 {since=beta13}
name: Protein ID (EMBL/GenBank/DDBJ)
namespace: identifier
subset: identifiers
subset: data
def: "EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators." [http://edamontology.org]
comment: This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.
is_a: EDAM_data:2907 ! Protein accession



[Term]
id: EDAM_data:2398
name: Protein ID (Ensembl)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a protein from the Ensembl database." [http://edamontology.org]
synonym: "Ensembl protein ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession
is_a: EDAM_data:2610 ! Ensembl ID


[Term]
id: EDAM_data:2713
name: Protein ID (CORUM)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a protein complex from the CORUM database." [http://edamontology.org]
synonym: "CORUM complex ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2715
name: Protein ID (CuticleDB)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a protein from the CuticleDB database." [http://edamontology.org]
synonym: "CuticleDB ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2723
name: Protein ID (DisProt)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a protein from the DisProt database." [http://edamontology.org]
synonym: "DisProt ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2789
name: Protein ID (TopDB)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a membrane protein from the TopDB database." [http://edamontology.org]
synonym: "TopDB ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2792
name: Protein ID (PeroxiBase)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a peroxidase protein from the PeroxiBase database." [http://edamontology.org]
synonym: "PeroxiBase ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2797
name: Protein ID (LGICdb)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a ligand-gated ion channel protein from the LGICdb database." [http://edamontology.org]
synonym: "LGICdb ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2617
name: Signaling Gateway protein ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database." [http://edamontology.org]
regex: "A[0-9]{6}"
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2647
name: LGICdb identifier
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database." [http://edamontology.org]
regex: "[a-zA-Z_0-9]+"
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2654
name: Target ID (TTD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a target protein from the Therapeutic Target Database (TTD)." [http://edamontology.org]
regex: "TTDS[0-9]+"
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2756
name: TCID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a membrane transport proteins from the transport classification database (TCDB)." [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:2772
name: HPA antibody id
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a antibody from the HPA database." [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2773
name: IMGT/HLA ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database." [http://edamontology.org]
is_a: EDAM_data:2907 ! Protein accession

[Term]
id: EDAM_data:2764
name: Protein name (UniProt)
namespace: identifier
subset: identifiers
subset: data
def: "Official name of a protein as used in the UniProt database." [http://edamontology.org]
is_a: EDAM_data:1009 ! Protein name

[Term]
id: EDAM_data:2775
name: Kinase name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a kinase protein." [http://edamontology.org]
is_a: EDAM_data:1009 ! Protein name

[Term]
id: EDAM_data:2321
name: Enzyme ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique, persistent identifier of an enzyme." [http://edamontology.org]
synonym: "Enzyme accession" EXACT [http://edamontology.org]
is_a: EDAM_data:1010 ! Enzyme identifier
is_a: EDAM_data:2907 ! Protein accession


[Term]
id: EDAM_data:1012
name: Enzyme name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an enzyme." [http://edamontology.org]
is_a: EDAM_data:1010 ! Enzyme identifier
is_a: EDAM_data:1009 ! Protein name


[Term]
id: EDAM_data:1011
name: EC number
namespace: identifier
subset: identifiers
subset: data
def: "An Enzyme Commission (EC) number of an enzyme." [http://edamontology.org]
synonym: "EC code" EXACT [http://edamontology.org]
synonym: "EC" EXACT [http://edamontology.org]
synonym: "Enzyme Commission number" EXACT [http://edamontology.org]
xref: Moby:EC_Number
xref: Moby:Annotated_EC_Number
regex: "[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+"
is_a: EDAM_data:2321 ! Enzyme ID

[Term]
id: EDAM_data:2107
name: Enzyme ID (BioCyc)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an enzyme from the BioCyc enzymes database." [http://edamontology.org]
synonym: "BioCyc enzyme ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2104 ! BioCyc ID
is_a: EDAM_data:2321 ! Enzyme ID

[Term]
id: EDAM_data:2629
name: Enzyme ID (MEROPS)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a peptidase enzyme from the MEROPS database." [http://edamontology.org]
synonym: "MEROPS ID" EXACT [http://edamontology.org]
regex: "S[0-9]{2}\.[0-9]{3}"
is_a: EDAM_data:2321 ! Enzyme ID

[Term]
id: EDAM_data:2702
name: Enzyme ID (CAZy)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an enzyme from the CAZy enzymes database." [http://edamontology.org]
synonym: "CAZy ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2321 ! Enzyme ID

[Term]
id: EDAM_data:2325
name: REBASE enzyme number
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org]
is_a: EDAM_data:2321 ! Enzyme ID


[Term]
id: EDAM_data:1013
name: Restriction enzyme name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a restriction enzyme." [http://edamontology.org]
is_a: EDAM_data:1012 ! Enzyme name
relationship: is_identifier_of EDAM_data:1517 ! Restriction enzyme property

[Term]
id: EDAM_data:1018
name: Nucleic acid feature identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of an nucleic acid feature." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1015 ! Sequence feature ID

[Term]
id: EDAM_data:1019
name: Protein feature identifier
namespace: identifier
subset: identifiers
subset: data
def: "Name or other identifier of a protein feature." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1015 ! Sequence feature ID


[Term]
id: EDAM_data:2736
name: Sequence feature ID (SwissRegulon)
namespace: identifier
subset: identifiers
subset: data
def: "A feature identifier as used in the SwissRegulon database." [http://edamontology.org]
comment: This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".
is_a: EDAM_data:1015 ! Sequence feature ID

[Term]
id: EDAM_data:1024
name: Codon name
namespace: identifier
subset: identifiers
subset: data
def: "String of one or more ASCII characters representing a codon." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1276 ! Nucleic acid features


! Don't know whether the loci identifiers listed here are 'ordered' or not.

[Term]
id: EDAM_data:2009
name: Ordered locus name
namespace: identifier
subset: identifiers
subset: data
def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:1895
name: Locus ID (AGI)
namespace: identifier
subset: identifiers
subset: data
def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [http://edamontology.org]
synonym: "AGI locus code" EXACT [http://edamontology.org]
synonym: "AGI ID" EXACT [http://edamontology.org]
synonym: "AGI identifier" EXACT [http://edamontology.org]
synonym: "Arabidopsis gene loci number" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode
regex: "AT[1-5]G[0-9]{5}"
is_a: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:1896
name: Locus ID (ASPGD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
is_a: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:1897
name: Locus ID (MGG)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1898
name: Locus ID (CGD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for loci from CGD (Candida Genome Database)." [http://edamontology.org]
synonym: "CGD locus identifier" EXACT [http://edamontology.org]
synonym: "CGDID" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD
xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1899
name: Locus ID (CMR)
namespace: identifier
subset: identifiers
subset: data
def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1900
name: NCBI locus tag
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for loci from NCBI database." [http://edamontology.org]
synonym: "Locus ID (NCBI)" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
xref: Moby_namespace:LocusID
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1901
name: Locus ID (SGD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [http://edamontology.org]
synonym: "SGDID" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD
xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
is_a: EDAM_data:1893 ! Locus ID
is_a: EDAM_data:2632 ! SGD ID


[Term]
id: EDAM_data:1902
name: Locus ID (MMP)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of loci from Maize Mapping Project." [http://edamontology.org]
xref: Moby_namespace:MMP_Locus
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1903
name: Locus ID (DictyBase)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [http://edamontology.org]
xref: Moby_namespace:DDB_gene
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1904
name: Locus ID (EntrezGene)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a locus from EntrezGene database." [http://edamontology.org]
xref: Moby_namespace:EntrezGene_EntrezGeneID
xref: Moby_namespace:EntrezGene_ID
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1905
name: Locus ID (MaizeGDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of locus from MaizeGDB (Maize genome database)." [http://edamontology.org]
xref: Moby_namespace:MaizeGDB_Locus
is_a: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:1908
name: Locus ID (Tropgene)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a locus from the Tropgene database." [http://edamontology.org]
xref: Moby:Tropgene_locus
is_a: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:2744
name: Locus ID (PseudoCAP)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a locus from the PseudoCAP database." [http://edamontology.org]
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:2745
name: Locus ID (UTR)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a locus from the UTR database." [http://edamontology.org]
is_a: EDAM_data:1893 ! Locus ID

[Term]
id: EDAM_data:2794
name: ORF ID
namespace: identifier
subset: identifiers
subset: data
def: "Accession of an open reading frame (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:2795 ! ORF identifier
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1026
name: Gene symbol
namespace: identifier
subset: identifiers
subset: data
def: "The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name." [http://edamontology.org]
xref: Moby_namespace:Global_GeneSymbol
xref: Moby_namespace:Global_GeneCommonName
is_a: EDAM_data:2299 ! Gene name

[Term]
id: EDAM_data:2299
name: Gene name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [http://edamontology.org]
is_a: EDAM_data:1025 ! Gene identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:2295
name: Gene ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [http://edamontology.org]
synonym: "Gene code" EXACT [http://edamontology.org]
synonym: "Gene accession" EXACT [http://edamontology.org]
is_a: EDAM_data:1025 ! Gene identifier
is_a: EDAM_data:1893 ! Locus ID


[Term]
id: EDAM_data:1891
name: iHOP symbol
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a protein or gene used in the iHOP database." [http://edamontology.org]
xref: Moby_namespace:iHOPsymbol
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2907 ! Protein accession
is_a: EDAM_data:2109 ! Identifier (hybrid)


! Suspect this identifiers more than just genes

[Term]
id: EDAM_data:1036
name: TIGR identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the TIGR database." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2109 ! Identifier (hybrid)

[Term]
id: EDAM_data:1037
name: TAIR accession (gene)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an gene from the TAIR database." [http://edamontology.org]
regex: "Gene:[0-9]{7}"
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2387 ! TAIR accession

[Term]
id: EDAM_data:2388
name: TAIR accession (At gene)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an Arabidopsis thaliana gene from the TAIR database." [http://edamontology.org]
is_a: EDAM_data:1037 ! TAIR accession (gene)

[Term]
id: EDAM_data:1806
name: Gene synonym
namespace: identifier
subset: identifiers
subset: data
def: "Any name (other than the recommended one) for a gene." [http://edamontology.org]
synonym: "Gene name synonym" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1026 ! Gene symbol


[Term]
id: EDAM_data:1807
name: ORF name
namespace: identifier
subset: identifiers
subset: data
def: "The name of an open reading frame attributed by a sequencing project." [http://edamontology.org]
is_a: EDAM_data:2795 ! ORF identifier
is_a: EDAM_data:2099 ! Name


! GeneFarm gene ID is also given

[Term]
id: EDAM_data:1892
name: Gene name (GeneFarm)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from the GeneFarm database." [http://edamontology.org]
xref: Moby_namespace:GENEFARM_GeneName
is_a: EDAM_data:1026 ! Gene symbol


[Term]
id: EDAM_data:1889
name: Gene name (DragonDB)
namespace: identifier
subset: identifiers
subset: data
def: "The name of an Antirrhinum Gene from the DragonDB database." [http://edamontology.org]
xref: Moby_namespace:DragonDB_Gene
is_a: EDAM_data:1026 ! Gene symbol


[Term]
id: EDAM_data:1890
name: Gene name (Arabidopsis)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [http://edamontology.org]
xref: Moby_namespace:ArabidopsisGeneSymbol
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1783
name: Gene name (ASPGD)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from Aspergillus Genome Database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1784
name: Gene name (CGD)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from Candida Genome Database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1785
name: Gene name (dictyBase)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from dictyBase database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1786
name: Gene name (EcoGene primary)
namespace: identifier
subset: identifiers
subset: data
def: "Primary name of a gene from EcoGene Database." [http://edamontology.org]
synonym: "EcoGene primary gene name" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1787
name: Gene name (MaizeGDB)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from MaizeGDB (maize genes) database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1788
name: Gene name (SGD)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from Saccharomyces Genome Database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS
is_a: EDAM_data:1026 ! Gene symbol
is_a: EDAM_data:2632 ! SGD ID

[Term]
id: EDAM_data:1789
name: Gene name (TGD)
namespace: identifier
subset: identifiers
subset: data
def: "Name of a gene from Tetrahymena Genome Database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1790
name: Gene name (CGSC)
namespace: identifier
subset: identifiers
subset: data
def: "Symbol of a gene from E.coli Genetic Stock Center." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1791
name: Gene name (HGNC)
namespace: identifier
subset: identifiers
subset: data
def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org]
synonym: "Official gene name" EXACT [http://edamontology.org]
synonym: "Gene name (HUGO)" EXACT [http://edamontology.org]
synonym: "HGNC symbol" EXACT [http://edamontology.org]
synonym: "HUGO symbol" EXACT [http://edamontology.org]
synonym: "HGNC gene symbol" EXACT [http://edamontology.org]
synonym: "HUGO gene symbol" EXACT [http://edamontology.org]
synonym: "HUGO gene name" EXACT [http://edamontology.org]
synonym: "HGNC gene name" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
regex: "HGNC:[0-9]{1,5}"
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1792
name: Gene name (MGD)
namespace: identifier
subset: identifiers
subset: data
def: "Symbol of a gene from the Mouse Genome Database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD
regex: "MGI:[0-9]+"
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:1793
name: Gene name (Bacillus subtilis)
namespace: identifier
subset: identifiers
subset: data
def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:2103
name: Gene name (KEGG GENES)
namespace: identifier
subset: identifiers
subset: data
def: "Name of an entry (gene) from the KEGG GENES database." [http://edamontology.org]
synonym: "KEGG GENES entry name" EXACT [http://edamontology.org]
xref: Moby_namespace:GeneId
regex: "[a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]*"
is_a: EDAM_data:1026 ! Gene symbol
is_a: EDAM_data:1154 ! KEGG object identifier

[Term]
id: EDAM_data:2296
name: Gene name (AceView)
namespace: identifier
subset: identifiers
subset: data
def: "Name of an entry (gene) from the AceView genes database." [http://edamontology.org]
synonym: "AceView gene name" EXACT [http://edamontology.org]
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:2300
name: Gene name (NCBI)
namespace: identifier
subset: identifiers
subset: data
def: "Name of an entry (gene) from the NCBI genes database." [http://edamontology.org]
synonym: "NCBI gene name" EXACT [http://edamontology.org]
is_a: EDAM_data:1026 ! Gene symbol


[Term]
id: EDAM_data:2740
name: Gene name (Genolist)
namespace: identifier
subset: identifiers
subset: data
def: "Name of an entry (gene) from the Genolist genes database." [http://edamontology.org]
synonym: "Genolist gene name" EXACT [http://edamontology.org]
is_a: EDAM_data:1026 ! Gene symbol

[Term]
id: EDAM_data:2743
name: Gene name (HUGO)
namespace: identifier
subset: identifiers
subset: data
def: "Name of an entry (gene) from the HUGO database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1791 ! Gene name (HGNC)


[Term]
id: EDAM_data:2771
name: HIX ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene cluster in the H-InvDB database." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2737
name: FIG ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene in the NMPDR database." [http://edamontology.org]
comment: A FIG ID consists of four parts: a prefix, genome id, locus type and id number.
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2774
name: Gene ID (JCVI)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI)." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2738
name: Gene ID (Xenbase)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene in the Xenbase database." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2799
name: Gene ID (MfunGD)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene in the MfunGD database." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2739
name: Gene ID (Genolist)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of gene in the Genolist database." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1028
name: Gene identifier (NCBI RefSeq)
namespace: identifier
subset: identifiers
subset: data
def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1027 ! Gene ID (NCBI)

[Term]
id: EDAM_data:1029
name: Gene identifier (NCBI UniGene)
namespace: identifier
subset: identifiers
subset: data
def: "An NCBI UniGene unique identifier of a gene." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1104 ! Sequence cluster ID (UniGene)

[Term]
id: EDAM_data:1030
name: Gene identifier (Entrez)
namespace: identifier
subset: identifiers
subset: data
def: "An Entrez unique identifier of a gene." [http://edamontology.org]
regex: "[0-9]+"
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1027 ! Gene ID (NCBI)


[Term]
id: EDAM_data:1886
name: Blattner number
namespace: identifier
subset: identifiers
subset: data
def: "The blattner identifier for a gene." [http://edamontology.org]
xref: Moby_namespace:Blattner_number
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:1027
name: Gene ID (NCBI)
namespace: identifier
subset: identifiers
subset: data
def: "An NCBI unique identifier of a gene." [http://edamontology.org]
synonym: "Gene identifier (NCBI)" EXACT [http://edamontology.org]
synonym: "NCBI gene ID" EXACT [http://edamontology.org]
synonym: "NCBI geneid" EXACT [http://edamontology.org]
synonym: "Gene identifier (Entrez)" EXACT [http://edamontology.org]
synonym: "Entrez gene ID" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene
xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:1098 ! RefSeq accession

[Term]
id: EDAM_data:1031
name: Gene ID (CGD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene or feature from the CGD database." [http://edamontology.org]
synonym: "CGD ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1032
name: Gene ID (DictyBase)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from DictyBase." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1033
name: Gene ID (Ensembl)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier for a gene (or other feature) from the Ensembl database." [http://edamontology.org]
synonym: "Ensembl Gene ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2610 ! Ensembl ID


[Term]
id: EDAM_data:1034
name: Gene ID (SGD)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the SGD database." [http://edamontology.org]
synonym: "SGD identifier" EXACT [http://edamontology.org]
regex: "S[0-9]+"
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2632 ! SGD ID


[Term]
id: EDAM_data:1885
name: Gene ID (GeneFarm)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from the GeneFarm database." [http://edamontology.org]
xref: Moby_namespace:GENEFARM_GeneID
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1907
name: Gene ID (KOME)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from the KOME database." [http://edamontology.org]
xref: Moby_namespace:GeneId
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1794
name: Gene ID (PlasmoDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1795
name: Gene ID (EcoGene)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from EcoGene Database." [http://edamontology.org]
synonym: "EcoGene Accession" EXACT [http://edamontology.org]
synonym: "EcoGene ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2297
name: Gene ID (ECK)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an E. coli K-12 gene from EcoGene Database." [http://edamontology.org]
synonym: "E. coli K-12 gene identifier" EXACT [http://edamontology.org]
synonym: "ECK accession" EXACT [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK
is_a: EDAM_data:1795 ! Gene ID (EcoGene)

[Term]
id: EDAM_data:1796
name: Gene ID (FlyBase)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from FlyBase database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB
xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:1802
name: Gene ID (Gramene)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Gramene database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1803
name: Gene ID (Virginia microbial)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1804
name: Gene ID (SGN)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Sol Genomics Network." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1805
name: Gene ID (WormBase)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier used by WormBase database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB
xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
regex: "WBGene[0-9]{8}"
is_a: EDAM_data:2295 ! Gene ID
is_a: EDAM_data:2113 ! WormBase identifier


[Term]
id: EDAM_data:1035
name: Gene ID (GeneDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a gene from the GeneDB database." [http://edamontology.org]
synonym: "GeneDB identifier" EXACT [http://edamontology.org]
xref: Moby_namespace:GeneDB
regex: "[a-zA-Z_0-9\.-]*"
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2285
name: Gene ID (MIPS)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for genetic elements in MIPS database." [http://edamontology.org]
synonym: "MIPS genetic element identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2298
name: Gene ID (HGNC)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [http://edamontology.org]
synonym: "HGNC ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2642
name: Gene ID (miRBase)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for a gene from the miRBase database." [http://edamontology.org]
synonym: "miRNA name" EXACT [http://edamontology.org]
synonym: "miRNA identifier" EXACT [http://edamontology.org]
synonym: "miRNA ID" EXACT [http://edamontology.org]
regex: "MI[0-9]{7}"
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2643
name: Gene ID (ZFIN)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for a gene from the Zebrafish information network genome (ZFIN) database." [http://edamontology.org]
regex: "ZDB\-GENE\-[0-9]+\-[0-9]+"
is_a: EDAM_data:2295 ! Gene ID

[Term]
id: EDAM_data:2759
name: Gene ID (VectorBase)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for a gene from the VectorBase database." [http://edamontology.org]
synonym: "VectorBase ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2835
name: Gene ID (VBASE2)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for a gene from the VBASE2 database." [http://edamontology.org]
synonym: "VBASE2 ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:1797
name: Gene ID (GeneDB Glossina morsitans)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Glossina morsitans GeneDB database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans
is_obsolete: true !{since=beta13}
consider: EDAM_data:1035 ! Gene ID (GeneDB)


[Term]
id: EDAM_data:1798
name: Gene ID (GeneDB Leishmania major)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Leishmania major GeneDB database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor
is_obsolete: true !{since=beta13}
consider: EDAM_data:1035 ! Gene ID (GeneDB)


[Term]
id: EDAM_data:1799
name: Gene ID (GeneDB Plasmodium falciparum)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Plasmodium falciparum GeneDB database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
is_obsolete: true !{since=beta13}
consider: EDAM_data:1035 ! Gene ID (GeneDB)


[Term]
id: EDAM_data:1800
name: Gene ID (GeneDB Schizosaccharomyces pombe)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
is_obsolete: true !{since=beta13}
consider: EDAM_data:1035 ! Gene ID (GeneDB)


[Term]
id: EDAM_data:1801
name: Gene ID (GeneDB Trypanosoma brucei)
namespace: identifier
subset: identifiers
subset: data
def: "Gene identifier from Trypanosoma brucei GeneDB database." [http://edamontology.org]
xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
is_obsolete: true !{since=beta13}
consider: EDAM_data:1035 ! Gene ID (GeneDB)

[Term]
id: EDAM_data:1887
name: Gene ID (MIPS Maize)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for genetic elements in MIPS Maize database." [http://edamontology.org]
synonym: "MIPS genetic element identifier (Maize)" EXACT [http://edamontology.org]
xref: Moby_namespace:MIPS_GE_Maize
is_obsolete: true !{since=beta13}
consider: EDAM_data:2285 ! Gene ID (MIPS)


[Term]
id: EDAM_data:1888
name: Gene ID (MIPS Medicago)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier for genetic elements in MIPS Medicago database." [http://edamontology.org]
synonym: "MIPS genetic element identifier (Medicago)" EXACT [http://edamontology.org]
xref: Moby_namespace:MIPS_GE_Medicago
is_obsolete: true !{since=beta13}
consider: EDAM_data:2285 ! Gene ID (MIPS)

[Term]
id: EDAM_data:2751
name: GenomeReviews ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a particular genome." [http://edamontology.org]
is_a: EDAM_data:2903 ! Genome accession


[Term]
id: EDAM_data:2786
name: NCBI Genome Project ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a genome project assigned by NCBI." [http://edamontology.org]
is_a: EDAM_data:2903 ! Genome accession


[Term]
id: EDAM_data:2787
name: NCBI genome accession
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a whole genome assigned by the NCBI." [http://edamontology.org]
is_a: EDAM_data:2903 ! Genome accession


[Term]
id: EDAM_data:2631
name: ACLAME ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a mobile genetic element from the Aclame database." [http://edamontology.org]
regex: "mge:[0-9]+"
is_a: EDAM_data:2630 ! Mobile genetic element ID

[Term]
id: EDAM_data:2128
name: Genetic code name
namespace: identifier
subset: identifiers
subset: data
def: "Informal name for a genetic code, typically an organism name." [http://edamontology.org]
is_a: EDAM_data:2127 ! Genetic code identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:1039
name: SCOP domain identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein domain (or other node) from the SCOP database." [http://edamontology.org]
is_a: EDAM_data:1038 ! Protein domain ID
relationship: is_identifier_of EDAM_data:1554 ! SCOP node

[Term]
id: EDAM_data:2700
name: CATH identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein domain (or other node) from the CATH database." [http://edamontology.org]
is_a: EDAM_data:1038 ! Protein domain ID
relationship: is_identifier_of EDAM_data:1553 ! CATH node


[Term]
id: EDAM_data:2666
name: CDD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a conserved domain from the Conserved Domain Database." [http://edamontology.org]
regex: "cd[0-9]{5}"
is_a: EDAM_data:1038 ! Protein domain ID

[Term]
id: EDAM_data:1041
name: SCOP concise classification string (sccs)
namespace: identifier
subset: identifiers
subset: data
def: "A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification." [http://edamontology.org]
comment: An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.
is_a: EDAM_data:1039 ! SCOP domain identifier

[Term]
id: EDAM_data:1042
name: SCOP sunid
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [http://edamontology.org]
comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.
example: "33229"
synonym: "sunid" EXACT [http://edamontology.org]
synonym: "SCOP unique identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1039 ! SCOP domain identifier

[Term]
id: EDAM_data:1040
name: CATH domain ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein domain from CATH." [http://edamontology.org]
example: "1nr3A00"
synonym: "CATH domain identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2700 ! CATH identifier

[Term]
id: EDAM_data:1043
name: CATH node ID
namespace: identifier
subset: identifiers
subset: data
def: "A code number identifying a node from the CATH database." [http://edamontology.org]
example: "3.30.1190.10.1.1.1.1.1"
synonym: "CATH code" EXACT [http://edamontology.org]
synonym: "CATH node identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2700 ! CATH identifier

[Term]
id: EDAM_data:2701
name: CATH node ID (family)
namespace: identifier
subset: identifiers
subset: data
def: "A code number identifying a family from the CATH database." [http://edamontology.org]
example: "2.10.10.10"
is_a: EDAM_data:1043 ! CATH node ID
relationship: is_identifier_of EDAM_data:1553 ! CATH node

[Term]
id: EDAM_data:2619
name: RESID ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein modification catalogued in the RESID database." [http://edamontology.org]
regex: "AA[0-9]{4}"
is_a: EDAM_data:2618 ! Protein modification ID

[Term]
id: EDAM_data:2892
name: Cell type name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a type or group of cells." [http://edamontology.org]
is_a: EDAM_data:2655 ! Cell type identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2656
name: NeuronDB ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a neuron from the NeuronDB database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2893 ! Cell type accession

[Term]
id: EDAM_data:2657
name: NeuroMorpho ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a neuron from the NeuroMorpho database." [http://edamontology.org]
regex: "[a-zA-Z_0-9]+"
is_a: EDAM_data:2893 ! Cell type accession


[Term]
id: EDAM_data:1868
name: Taxon
namespace: identifier
subset: identifiers
subset: data
def: "The name of a group of organisms belonging to the same taxonomic rank." [http://edamontology.org]
comment: For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
synonym: "Taxonomy rank" EXACT [http://edamontology.org]
synonym: "Taxonomic rank" EXACT [http://edamontology.org]
xref: Moby:BriefTaxonConcept
xref: Moby:PotentialTaxon
is_a: EDAM_data:2909 ! Organism name

[Term]
id: EDAM_data:1872
name: Taxonomic classification
namespace: identifier
subset: identifiers
subset: data
def: "The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature." [http://edamontology.org]
comment: Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.
synonym: "Taxonomic name" EXACT [http://edamontology.org]
synonym: "Taxonomic information" EXACT [http://edamontology.org]
xref: Moby:GCP_Taxon
xref: Moby:TaxonName
xref: Moby:TaxonTCS
xref: Moby:TaxonScientificName
xref: Moby:iANT_organism-xml
is_a: EDAM_data:2909 ! Organism name

[Term]
id: EDAM_data:1874
name: Genbank common name
namespace: identifier
subset: identifiers
subset: data
def: "Common name for an organism as used in the GenBank database." [http://edamontology.org]
is_a: EDAM_data:2909 ! Organism name

[Term]
id: EDAM_data:1873
name: iHOP organism ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for an organism used in the iHOP database." [http://edamontology.org]
xref: Moby_namespace:iHOPorganism
is_a: EDAM_data:2908 ! Organism accession


[Term]
id: EDAM_data:2102
name: KEGG organism code
namespace: identifier
subset: identifiers
subset: data
def: "A three-letter code used in the KEGG databases to uniquely identify organisms." [http://edamontology.org]
is_a: EDAM_data:2909 ! Organism name
is_a: EDAM_data:1154 ! KEGG object identifier


[Term]
id: EDAM_data:2593
name: BRENDA organism ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for an organism used in the BRENDA database." [http://edamontology.org]
is_a: EDAM_data:2908 ! Organism accession


[Term]
id: EDAM_data:2913
name: Virus identifier
namespace: identifier
subset: identifiers
subset: data
def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:1869 ! Organism identifier
relationship: is_identifier_of EDAM_data:2307 ! Virus annotation

[Term]
id: EDAM_data:2785
name: Virus ID
namespace: identifier
subset: identifiers
subset: data
def: "An accession of annotation on a (group of) viruses (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:2913 ! Virus identifier
is_a: EDAM_data:2908 ! Organism accession


[Term]
id: EDAM_data:2836
name: DPVweb ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for a virus from the DPVweb database." [http://edamontology.org]
synonym: "DPVweb virus ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2785 ! Virus ID

[Term]
id: EDAM_data:2784
name: RNAVirusDB ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for a virus from the RNAVirusDB database." [http://edamontology.org]
is_a: EDAM_data:2785 ! Virus ID

! Could list (or cross-reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.

[Term]
id: EDAM_data:1875
name: NCBI taxon
namespace: identifier
subset: identifiers
subset: data
def: "The name of a taxon from the NCBI taxonomy database." [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon


[Term]
id: EDAM_data:2594
name: UniGene taxon
namespace: identifier
subset: identifiers
subset: data
def: "The name of a taxon using the controlled vocabulary of the UniGene database." [http://edamontology.org]
synonym: "UniGene organism abbreviation" EXACT [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon

[Term]
id: EDAM_data:2595
name: UTRdb taxon
namespace: identifier
subset: identifiers
subset: data
def: "The name of a taxon using the controlled vocabulary of the UTRdb database." [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon

[Term]
id: EDAM_data:1044
name: Kingdom name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes)." [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon

[Term]
id: EDAM_data:1870
name: Genus name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a genus of organism." [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon


[Term]
id: EDAM_data:2732
name: Family name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a family of organism." [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon

[Term]
id: EDAM_data:1045
name: Species name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a species (typically a taxonomic group) of organism." [http://edamontology.org]
synonym: "Organism species" EXACT [http://edamontology.org]
is_a: EDAM_data:1868 ! Taxon


[Term]
id: EDAM_data:2733
name: Genus name (virus)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a genus of viruses." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1870 ! Genus name

[Term]
id: EDAM_data:2734
name: Family name (virus)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a family of viruses." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:2732 ! Family name


[Term]
id: EDAM_data:2317
name: Cell line name (exact)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a cell line." [http://edamontology.org]
is_a: EDAM_data:2316 ! Cell line name

[Term]
id: EDAM_data:2318
name: Cell line name (truncated)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a cell line." [http://edamontology.org]
is_a: EDAM_data:2316 ! Cell line name

[Term]
id: EDAM_data:2319
name: Cell line name (no punctuation)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a cell line." [http://edamontology.org]
is_a: EDAM_data:2316 ! Cell line name

[Term]
id: EDAM_data:2320
name: Cell line name (assonant)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a cell line." [http://edamontology.org]
is_a: EDAM_data:2316 ! Cell line name

[Term]
id: EDAM_data:1056
name: Database name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a biological or bioinformatics database." [http://edamontology.org]
is_a: EDAM_data:1048 ! Database identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2149
name: Database category name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a category of biological or bioinformatics database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1056 ! Database name

[Term]
id: EDAM_data:1057
name: Sequence database name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a molecular sequence database." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1056 ! Database name

[Term]
id: EDAM_data:2735
name: Database name (SwissRegulon)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a SwissRegulon database." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1056 ! Database name


[Term]
id: EDAM_data:2747
name: Database name (CMD)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a subdivision of the Collagen Mutation Database (CMD) database." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1056 ! Database name


[Term]
id: EDAM_data:2748
name: Database name (Osteogenesis)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a subdivision of the Osteogenesis database." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_data:1056 ! Database name

[Term]
id: EDAM_data:1058
name: Enumerated file name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a file (of any type) with restricted possible values." [http://edamontology.org]
is_a: EDAM_data:1050 ! File name

[Term]
id: EDAM_data:1059
name: File name extension
namespace: identifier
subset: identifiers
subset: data
def: "The extension of a file name." [http://edamontology.org]
comment: A file extension is the characters appearing after the final '.' in the file name.
is_a: EDAM_data:1050 ! File name

[Term]
id: EDAM_data:1060
name: File base name
namespace: identifier
subset: identifiers
subset: data
def: "The base name of a file." [http://edamontology.org]
comment: A file base name is the file name stripped of its directory specification and extension.
is_a: EDAM_data:1050 ! File name


[Term]
id: EDAM_data:1061
name: QSAR descriptor name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a QSAR descriptor." [http://edamontology.org]
is_a: EDAM_data:2110 ! Molecular property identifier
is_a: EDAM_data:2099 ! Name
relationship: is_identifier_of EDAM_data:0847 ! QSAR descriptor


[Term]
id: EDAM_data:2288
name: Sequence identifier (protein)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of protein sequence(s) or protein sequence database entries." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1096 ! Sequence accession (protein)


[Term]
id: EDAM_data:2289
name: Sequence identifier (nucleic acid)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1097 ! Sequence accession (nucleic acid)


[Term]
id: EDAM_data:1093
name: Sequence accession
namespace: identifier
subset: identifiers
subset: data
def: "A persistent, unique identifier of a molecular sequence database entry." [http://edamontology.org]
synonym: "Sequence accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1063 ! Sequence identifier
is_a: EDAM_data:2091 ! Accession
is_a: EDAM_data:2914 ! Sequence features metadata


[Term]
id: EDAM_data:2154
name: Sequence name
namespace: identifier
subset: identifiers
subset: data
def: "Any arbitrary name of a molecular sequence." [http://edamontology.org]
is_a: EDAM_data:1063 ! Sequence identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:1095
name: EMBOSS Uniform Sequence Address
namespace: identifier
subset: identifiers
subset: data
def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [http://edamontology.org]
synonym: "EMBOSS USA" EXACT [http://edamontology.org]
is_a: EDAM_data:1063 ! Sequence identifier
is_a: EDAM_data:2099 ! Name



[Term]
id: EDAM_data:2291
name: UniProt ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a polypeptide in the UniProt database." [http://edamontology.org]
synonym: "UniProt identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:1100
name: PIR identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of PIR sequence database entry." [http://edamontology.org]
synonym: "PIR accession number" EXACT [http://edamontology.org]
synonym: "PIR ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:1101
name: TREMBL accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a TREMBL sequence database entry." [http://edamontology.org]
is_a: EDAM_data:3021 ! UniProt accession
synonym: "TREMBL accession number" EXACT [http://edamontology.org]
synonym: "TREMBL ID" EXACT [http://edamontology.org]
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:2621
name: TAIR accession (protein)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org]
regex: "AASequence:[0-9]{10}"
is_a: EDAM_data:1096 ! Sequence accession (protein)
is_a: EDAM_data:2387 ! TAIR accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_data:2290
name: EMBL accession
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:1107
def: "An accession number of an entry from the EMBL sequence database." [http://edamontology.org]
synonym: "EMBL accession number" EXACT [http://edamontology.org]
synonym: "EMBL identifier" EXACT [http://edamontology.org]
synonym: "EMBL ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID


[Term]
id: EDAM_data:2292
name: GenBank accession
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:1108
def: "Accession number of an entry from the GenBank sequence database." [http://edamontology.org]
is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID
synonym: "GenBank accession number" EXACT [http://edamontology.org]
synonym: "GenBank identifier" EXACT [http://edamontology.org]
synonym: "GenBank ID" EXACT [http://edamontology.org]


[Term]
id: EDAM_data:2916
name: DDBJ accession
namespace: identifier
subset: identifiers
subset: data
! alt_id: EDAM_data:1109
def: "An identifier of an entry from the DDBJ sequence database." [http://edamontology.org]
is_a: EDAM_data:1103 ! EMBL/GenBank/DDBJ ID
synonym: "DDBJ accession number" EXACT [http://edamontology.org]
synonym: "DDBJ identifier" EXACT [http://edamontology.org]
synonym: "DDBJ ID" EXACT [http://edamontology.org]


[Term]
id: EDAM_data:1855
name: Clone ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a clone (cloned molecular sequence) from a database." [http://edamontology.org]
is_a: EDAM_data:2769 ! Transcript ID


[Term]
id: EDAM_data:2386
name: EPD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (promoter) from the EPD database." [http://edamontology.org]
synonym: "EPD identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2727 ! Promoter ID


[Term]
id: EDAM_data:2741
name: ABS ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry (promoter) from the ABS database." [http://edamontology.org]
synonym: "ABS identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2727 ! Promoter ID

[Term]
id: EDAM_data:1096
name: Sequence accession (protein)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a protein sequence database entry." [http://edamontology.org]
synonym: "Protein sequence accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:2976 ! Protein sequence

[Term]
id: EDAM_data:1097
name: Sequence accession (nucleic acid)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org]
synonym: "Nucleotide sequence accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence


[Term]
id: EDAM_data:2362
name: Sequence accession (hybrid)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a nucleotide or protein sequence database entry." [http://edamontology.org]
is_a: EDAM_data:1093 ! Sequence accession
relationship: is_identifier_of EDAM_data:0849 ! Sequence record


[Term]
id: EDAM_data:1098
name: RefSeq accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a RefSeq database entry." [http://edamontology.org]
regex: "(NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+"
is_a: EDAM_data:2362 ! Sequence accession (hybrid)
synonym: "RefSeq ID" EXACT [http://edamontology.org]

[Term]
id: EDAM_data:2314
name: GI number
namespace: identifier
subset: identifiers
subset: data
def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [http://edamontology.org]
comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
synonym: "NCBI GI number" EXACT [http://edamontology.org]
synonym: "gi number" EXACT [http://edamontology.org]
is_a: EDAM_data:2362 ! Sequence accession (hybrid)

[Term]
id: EDAM_data:2315
name: NCBI version
namespace: identifier
subset: identifiers
subset: data
def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [http://edamontology.org]
comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.
synonym: "accession.version" EXACT [http://edamontology.org]
synonym: "NCBI accession.version" EXACT [http://edamontology.org]
is_a: EDAM_data:2362 ! Sequence accession (hybrid)

[Term]
id: EDAM_data:2385
name: RefSeq accession (protein)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a protein from the RefSeq database." [http://edamontology.org]
is_a: EDAM_data:1098 ! RefSeq accession
synonym: "RefSeq protein ID" EXACT [http://edamontology.org]

[Term]
id: EDAM_data:2327
name: GI number (protein)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier assigned to NCBI protein sequence records." [http://edamontology.org]
comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
synonym: "protein gi number" EXACT [http://edamontology.org]
synonym: "protein gi" EXACT [http://edamontology.org]
is_a: EDAM_data:2314 ! GI number

[Term]
id: EDAM_data:1099
name: UniProt accession (extended)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org]
regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+"
example: "Q7M1G0" "P43353-2" "P01012.107"
! is_a: EDAM_data:3021 ! UniProt accession
! relationship: is_identifier_of EDAM_format:1208 ! Protein sequence ! now 'protein' format
! relationship: is_identifier_of EDAM_data:0849 ! Sequence record
is_obsolete: true !{since=1.0}
consider: EDAM_data:3021 ! UniProt accession

[Term]
id: EDAM_data:3021
name: UniProt accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a UniProt (protein sequence) database entry." [http://edamontology.org]
regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]"
example: "P43353" "Q7M1G0" "Q9C199" "A5A6J6"
synonym: "UniProtKB accession number" EXACT [http://edamontology.org]
synonym: "UniProtKB entry accession" EXACT [http://edamontology.org]
synonym: "UniProt accession number" EXACT [http://edamontology.org]
synonym: "Swiss-Prot accession" EXACT [http://edamontology.org]
is_a: EDAM_data:2291 ! UniProt ID
relationship: is_identifier_of EDAM_data:0849 ! Sequence record ! Of protein/peptide (feature) record? Also of a class of protein molecules?

[Term]
id: EDAM_data:2392
name: UniParc accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a UniParc (protein sequence) database entry." [http://edamontology.org]
synonym: "UniParc ID" EXACT [http://edamontology.org]
synonym: "UPI" EXACT [http://edamontology.org]
regex: "UPI[A-F0-9]{10}"
is_a: EDAM_data:2291 ! UniProt ID

[Term]
id: EDAM_data:2915
name: Gramene identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a Gramene database entry." [http://edamontology.org]
is_a: EDAM_data:1096 ! Sequence accession (protein)

[Term]
id: EDAM_data:1102
name: Gramene primary identifier
namespace: identifier
subset: identifiers
subset: data
def: "Primary identifier of a Gramene database entry." [http://edamontology.org]
synonym: "Gramene primary ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2915 ! Gramene identifier

[Term]
id: EDAM_data:2293
name: Gramene secondary identifier
namespace: identifier
subset: identifiers
subset: data
def: "Secondary (internal) identifier of a Gramene database entry." [http://edamontology.org]
synonym: "Gramene secondary ID" EXACT [http://edamontology.org]
synonym: "Gramene internal ID" EXACT [http://edamontology.org]
synonym: "Gramene internal identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2915 ! Gramene identifier

[Term]
id: EDAM_data:2384
name: IPI protein ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a protein entry catalogued in the International Protein Index (IPI) database." [http://edamontology.org]
regex: "IPI[0-9]{8}"
is_a: EDAM_data:1096 ! Sequence accession (protein)


[Term]
id: EDAM_data:2728
name: EST accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an EST sequence." [http://edamontology.org]
is_a: EDAM_data:1855 ! Clone ID

[Term]
id: EDAM_data:1103
name: EMBL/GenBank/DDBJ ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases." [http://edamontology.org]
is_a: EDAM_data:1097 ! Sequence accession (nucleic acid)

[Term]
id: EDAM_data:2389
name: UniSTS accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the UniSTS database." [http://edamontology.org]
is_a: EDAM_data:1097 ! Sequence accession (nucleic acid)

[Term]
id: EDAM_data:2390
name: UNITE accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the UNITE database." [http://edamontology.org]
is_a: EDAM_data:1097 ! Sequence accession (nucleic acid)

[Term]
id: EDAM_data:2391
name: UTR accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the UTR database." [http://edamontology.org]
is_a: EDAM_data:1097 ! Sequence accession (nucleic acid)

[Term]
id: EDAM_data:2393
name: mFLJ/mKIAA number
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the Rouge or HUGE databases." [http://edamontology.org]
is_a: EDAM_data:2295 ! Gene ID


[Term]
id: EDAM_data:2781
name: REDIdb ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the RNA editing database (REDIdb)." [http://edamontology.org]
is_a: EDAM_data:1097 ! Sequence accession (nucleic acid)


[Term]
id: EDAM_data:2729
name: COGEME EST ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an EST sequence from the COGEME database." [http://edamontology.org]
is_a: EDAM_data:2728 ! EST accession

[Term]
id: EDAM_data:2730
name: COGEME unisequence ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a unisequence from the COGEME database." [http://edamontology.org]
comment: A unisequence is a single sequence assembled from ESTs.
is_a: EDAM_data:2728 ! EST accession

[Term]
id: EDAM_data:2798
name: MaizeDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an EST sequence from the MaizeDB database." [http://edamontology.org]
is_a: EDAM_data:2728 ! EST accession


[Term]
id: EDAM_data:1105
name: dbEST accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a dbEST database entry." [http://edamontology.org]
synonym: "dbEST ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2292 ! GenBank accession
is_a: EDAM_data:2728 ! EST accession

[Term]
id: EDAM_data:2704
name: Clone ID (IMAGE)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence)." [http://edamontology.org]
synonym: "I.M.A.G.E. cloneID" EXACT [http://edamontology.org]
synonym: "IMAGE cloneID" EXACT [http://edamontology.org]
is_a: EDAM_data:1855 ! Clone ID


[Term]
id: EDAM_data:2803
name: Clone ID (RefSeq)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a cDNA molecule catalogued in the RefSeq database." [http://edamontology.org]
is_a: EDAM_data:1855 ! Clone ID
is_a: EDAM_data:1098 ! RefSeq accession

[Term]
id: EDAM_data:1110
name: EMBOSS sequence type
namespace: identifier
subset: identifiers
subset: data
def: "The EMBOSS type of a molecular sequence." [http://edamontology.org]
comment: See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1094 ! Sequence type

[Term]
id: EDAM_data:1106
name: dbSNP ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a dbSNP database entry." [http://edamontology.org]
synonym: "dbSNP identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2294 ! Sequence variation ID


[Term]
id: EDAM_data:2805
name: GeneSNP ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a GeneSNP database entry." [http://edamontology.org]
is_a: EDAM_data:2294 ! Sequence variation ID

[Term]
id: EDAM_data:1112
name: Sequence cluster ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a cluster of molecular sequence(s)." [http://edamontology.org]
is_a: EDAM_data:1064 ! Sequence set ID
relationship: is_identifier_of EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_data:2346
name: Sequence cluster ID (UniRef)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the UniRef database." [http://edamontology.org]
synonym: "UniRef entry accession" EXACT [http://edamontology.org]
synonym: "UniRef cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:1113
name: Sequence cluster ID (COG)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the COG database." [http://edamontology.org]
synonym: "COG ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:1104
name: Sequence cluster ID (UniGene)
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of an entry (gene cluster) from the NCBI UniGene database." [http://edamontology.org]
synonym: "UniGene ID" EXACT [http://edamontology.org]
synonym: "UniGene identifier" EXACT [http://edamontology.org]
synonym: "UniGene cluster ID" EXACT [http://edamontology.org]
synonym: "UniGene cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:2220
name: Sequence cluster ID (SYSTERS)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a sequence cluster from the SYSTERS database." [http://edamontology.org]
synonym: "SYSTERS cluster ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:2612
name: Sequence cluster ID (CluSTr)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a sequence cluster from the CluSTr database." [http://edamontology.org]
synonym: "CluSTr cluster ID" EXACT [http://edamontology.org]
synonym: "CluSTr ID" EXACT [http://edamontology.org]
regex: "[0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])?"
is_a: EDAM_data:1112 ! Sequence cluster ID

[Term]
id: EDAM_data:2347
name: Sequence cluster ID (UniRef100)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the UniRef100 database." [http://edamontology.org]
synonym: "UniRef100 entry accession" EXACT [http://edamontology.org]
synonym: "UniRef100 cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef)

[Term]
id: EDAM_data:2348
name: Sequence cluster ID (UniRef90)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the UniRef90 database." [http://edamontology.org]
synonym: "UniRef90 entry accession" EXACT [http://edamontology.org]
synonym: "UniRef90 cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef)

[Term]
id: EDAM_data:2349
name: Sequence cluster ID (UniRef50)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the UniRef50 database." [http://edamontology.org]
synonym: "UniRef50 entry accession" EXACT [http://edamontology.org]
synonym: "UniRef50 cluster id" EXACT [http://edamontology.org]
is_a: EDAM_data:2346 ! Sequence cluster ID (UniRef)


[Term]
id: EDAM_data:2761
name: UTRSite ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs." [http://edamontology.org]
is_a: EDAM_data:1114 ! Sequence motif identifier


[Term]
id: EDAM_data:1116
name: ELM ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the ELMdb database of protein functional sites." [http://edamontology.org]
is_a: EDAM_data:1114 ! Sequence motif identifier


[Term]
id: EDAM_data:1117
name: Prosite accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the Prosite database." [http://edamontology.org]
synonym: "Prosite ID" EXACT [http://edamontology.org]
regex: "PS[0-9]{5}"
is_a: EDAM_data:1114 ! Sequence motif identifier

[Term]
id: EDAM_data:2714
name: CDD PSSM-ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a position-specific scoring matrix from the CDD database." [http://edamontology.org]
is_a: EDAM_data:1115 ! Sequence profile ID


[Term]
id: EDAM_data:1118
name: HMMER hidden Markov model ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier or name of a HMMER hidden Markov model." [http://edamontology.org]
is_a: EDAM_data:1115 ! Sequence profile ID
relationship: is_identifier_of EDAM_data:1364 ! Hidden Markov model

[Term]
id: EDAM_data:1119
name: JASPAR profile ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier or name of a profile from the JASPAR database." [http://edamontology.org]
is_a: EDAM_data:1115 ! Sequence profile ID


[Term]
id: EDAM_data:2150
name: Sequence profile name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a sequence profile." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1115 ! Sequence profile ID

[Term]
id: EDAM_data:1123
name: TreeBASE study accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the TreeBASE database." [http://edamontology.org]
is_a: EDAM_data:1068 ! Phylogenetic tree ID

[Term]
id: EDAM_data:1124
name: TreeFam accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the TreeFam database." [http://edamontology.org]
is_a: EDAM_data:1068 ! Phylogenetic tree ID

[Term]
id: EDAM_data:1126
name: Comparison matrix name
namespace: identifier
subset: identifiers
subset: data
def: "Unique name or identifier of a comparison matrix." [http://edamontology.org]
comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
synonym: "Substitution matrix name" EXACT [http://edamontology.org]
is_a: EDAM_data:1069 ! Comparison matrix identifier
is_a: EDAM_data:2099 ! Name
relationship: is_identifier_of EDAM_data:0874 ! Comparison matrix


[Term]
id: EDAM_data:1127
name: PDB ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an entry from the PDB database." [http://edamontology.org]
synonym: "PDB identifier" EXACT [http://edamontology.org]
synonym: "PDBID" EXACT [http://edamontology.org]
regex: "[a-zA-Z_0-9]{4}"
is_a: EDAM_data:1070 ! Structure ID


[Term]
id: EDAM_data:2667
name: MMDB ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of an entry from the MMDB database." [http://edamontology.org]
synonym: "MMDB accession" EXACT [http://edamontology.org]
regex: "[0-9]{1,5}"
is_a: EDAM_data:1070 ! Structure ID


[Term]
id: EDAM_data:2793
name: SISYPHUS ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the SISYPHUS database of tertiary structure alignments." [http://edamontology.org]
is_a: EDAM_data:1072 ! Structure alignment ID


[Term]
id: EDAM_data:1128
name: AAindex ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the AAindex database." [http://edamontology.org]
is_a: EDAM_data:1073 ! Amino acid index ID

[Term]
id: EDAM_data:1074
name: Protein interaction ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a report of protein interactions from a protein interaction database (typically)." [http://edamontology.org]
is_a: EDAM_data:2627 ! Molecular interaction ID


[Term]
id: EDAM_data:2628
name: BioGRID interaction ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of an interaction from the BioGRID database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2627 ! Molecular interaction ID

[Term]
id: EDAM_data:2636
name: MatrixDB interaction ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of an interaction from the MatrixDB database." [http://edamontology.org]
regex: "([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)"
is_a: EDAM_data:2627 ! Molecular interaction ID

[Term]
id: EDAM_data:1129
name: BIND accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the BIND database." [http://edamontology.org]
is_a: EDAM_data:1074 ! Protein interaction ID

[Term]
id: EDAM_data:1130
name: IntAct accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the IntAct database." [http://edamontology.org]
regex: "EBI\-[0-9]+"
is_a: EDAM_data:1074 ! Protein interaction ID


[Term]
id: EDAM_data:2302
name: STRING ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [http://edamontology.org]
is_a: EDAM_data:1074 ! Protein interaction ID

[Term]
id: EDAM_data:2615
name: MINT ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the MINT database of protein-protein interactions." [http://edamontology.org]
regex: "MINT\-[0-9]{1,5}"
is_a: EDAM_data:1074 ! Protein interaction ID

[Term]
id: EDAM_data:2616
name: DIP ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the DIP database of protein-protein interactions." [http://edamontology.org]
regex: "DIP[\:\-][0-9]{3}[EN]"
is_a: EDAM_data:1074 ! Protein interaction ID

[Term]
id: EDAM_data:2668
name: iRefIndex ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the iRefIndex database of protein-protein interactions." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:1074 ! Protein interaction ID


[Term]
id: EDAM_data:1076
name: Codon usage table name
namespace: identifier
subset: identifiers
subset: data
def: "Unique name of a codon usage table." [http://edamontology.org]
is_a: EDAM_data:2111 ! Codon usage table identifier
is_a: EDAM_data:2099 ! Name
relationship: is_identifier_of EDAM_data:1597 ! Codon usage table
relationship: is_identifier_of EDAM_data:1598 ! Genetic code

[Term]
id: EDAM_data:2356
name: RFAM accession
namespace: identifier
subset: identifiers
subset: data
def: "Stable accession number of an entry (RNA family) from the RFAM database." [http://edamontology.org]
is_a: EDAM_data:2355 ! RNA family identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2606
name: RFAM name
namespace: identifier
subset: identifiers
subset: data
def: "Name (not necessarily stable) an entry (RNA family) from the RFAM database." [http://edamontology.org]
is_a: EDAM_data:2355 ! RNA family identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:2766
name: HAMAP ID
namespace: identifier
subset: identifiers
subset: data
def: "Name of a protein family from the HAMAP database." [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:1132
name: InterPro entry name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an InterPro entry, usually indicating the type of protein matches for that entry." [http://edamontology.org]
is_a: EDAM_data:1131 ! Protein family name
relationship: is_identifier_of EDAM_data:1355 ! Protein signature

[Term]
id: EDAM_data:1133
name: InterPro accession
namespace: identifier
subset: identifiers
subset: data
def: "Primary accession number of an InterPro entry." [http://edamontology.org]
comment: Every InterPro entry has a unique accession number to provide a persistent citation of database records.
synonym: "InterPro primary accession number" EXACT [http://edamontology.org]
synonym: "InterPro primary accession" EXACT [http://edamontology.org]
regex: "IPR[0-9]{6}"
example: "IPR015590"
is_a: EDAM_data:2910 ! Protein family accession
relationship: is_identifier_of EDAM_data:1355 ! Protein signature


[Term]
id: EDAM_data:1134
name: InterPro secondary accession
namespace: identifier
subset: identifiers
subset: data
def: "Secondary accession number of an InterPro entry." [http://edamontology.org]
synonym: "InterPro secondary accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:1133 ! InterPro accession
relationship: is_identifier_of EDAM_data:1355 ! Protein signature


[Term]
id: EDAM_data:1135
name: Gene3D ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the Gene3D database." [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:1136
name: PIRSF ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the PIRSF database." [http://edamontology.org]
regex: "PIRSF[0-9]{6}"
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:1137
name: PRINTS code
namespace: identifier
subset: identifiers
subset: data
def: "The unique identifier of an entry in the PRINTS database." [http://edamontology.org]
regex: "PR[0-9]{5}"
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:1138
name: Pfam accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a Pfam entry." [http://edamontology.org]
regex: "PF[0-9]{5}"
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:2758
name: Pfam clan ID
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of a Pfam clan." [http://edamontology.org]
regex: "CL[0-9]{4}"
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:2757
name: Pfam domain name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a domain from the Pfam database." [http://edamontology.org]
regex: "PF[0-9]{5}"
is_a: EDAM_data:1131 ! Protein family name


[Term]
id: EDAM_data:2782
name: SMART domain name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a domain from the SMART database." [http://edamontology.org]
is_a: EDAM_data:1131 ! Protein family name


[Term]
id: EDAM_data:1139
name: SMART accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the SMART database." [http://edamontology.org]
regex: "SM[0-9]{5}"
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:1140
name: Superfamily hidden Markov model number
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier (number) of a hidden Markov model from the Superfamily database." [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:1141
name: TIGRFam ID
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org]
synonym: "TIGRFam accession number" EXACT [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:1142
name: ProDom accession number
namespace: identifier
subset: identifiers
subset: data
def: "A ProDom domain family accession number." [http://edamontology.org]
comment: ProDom is a protein domain family database.
regex: "PD[0-9]+"
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:2614
name: TCDB ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins." [http://edamontology.org]
comment: OBO file for regular expression.
synonym: "TC number" EXACT [http://edamontology.org]
regex: "[0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+"
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:2731
name: Protein family ID (GeneFarm)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry (family) from the TIGRFam database." [http://edamontology.org]
synonym: "GeneFarm family ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession


[Term]
id: EDAM_data:2783
name: Protein family ID (PANTHER)
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry (family) from the PANTHER database." [http://edamontology.org]
synonym: "Panther family ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2910 ! Protein family accession

[Term]
id: EDAM_data:1143
name: TRANSFAC accession number
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the TRANSFAC database." [http://edamontology.org]
is_a: EDAM_data:2911 ! Transcription factor accession


[Term]
id: EDAM_data:2716
name: DBD ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a predicted transcription factor from the DBD database." [http://edamontology.org]
is_a: EDAM_data:2911 ! Transcription factor accession

[Term]
id: EDAM_data:2742
name: AraC-XylS ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a transcription factor from the AraC-XylS database." [http://edamontology.org]
is_a: EDAM_data:2911 ! Transcription factor accession

[Term]
id: EDAM_data:2755
name: Transcription factor name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a transcription factor." [http://edamontology.org]
is_a: EDAM_data:1077 ! Transcription factor identifier
is_a: EDAM_data:1009 ! Protein name

[Term]
id: EDAM_data:1144
name: ArrayExpress accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the ArrayExpress database." [http://edamontology.org]
synonym: "ArrayExpress experiment ID" EXACT [http://edamontology.org]
regex: "[AEP]-[a-zA-Z_0-9]{4}-[0-9]+"
is_a: EDAM_data:1078 ! Microarray experiment annotation ID


[Term]
id: EDAM_data:1145
name: PRIDE experiment accession number
namespace: identifier
subset: identifiers
subset: data
def: "PRIDE experiment accession number." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:1078 ! Microarray experiment annotation ID


[Term]
id: EDAM_data:2710
name: CleanEx dataset code
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database." [http://edamontology.org]
is_a: EDAM_data:1078 ! Microarray experiment annotation ID

[Term]
id: EDAM_data:1146
name: EMDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the EMDB electron microscopy database." [http://edamontology.org]
is_a: EDAM_data:1079 ! Electron microscopy model ID

[Term]
id: EDAM_data:1147
name: GEO accession number
namespace: identifier
subset: identifiers
subset: data
def: "Accession number of an entry from the GEO database." [http://edamontology.org]
regex: "o^GDS[0-9]+"
is_a: EDAM_data:1080 ! Gene expression report ID

[Term]
id: EDAM_data:1148
name: GermOnline ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the GermOnline database." [http://edamontology.org]
is_a: EDAM_data:1080 ! Gene expression report ID


[Term]
id: EDAM_data:1149
name: EMAGE ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the EMAGE database." [http://edamontology.org]
is_a: EDAM_data:1080 ! Gene expression report ID

[Term]
id: EDAM_data:2709
name: CleanEx entry name
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a gene expression profile from the CleanEx database." [http://edamontology.org]
is_a: EDAM_data:1080 ! Gene expression report ID

[Term]
id: EDAM_data:1150
name: Disease ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from a database of disease." [http://edamontology.org]
is_a: EDAM_data:0976 ! Identifier (typed)
is_a: EDAM_data:2091 ! Accession
relationship: is_identifier_of EDAM_data:1622 ! Disease annotation

[Term]
id: EDAM_data:1151
name: HGVbase ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the HGVbase database." [http://edamontology.org]
is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID

[Term]
id: EDAM_data:1152
name: HIVDB identifier
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the HIVDB database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:0842 ! Identifier


[Term]
id: EDAM_data:1153
name: OMIM ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the OMIM database." [http://edamontology.org]
regex: "[*#+%^]?[0-9]{6}"
is_a: EDAM_data:1081 ! Genotype and phenotype annotation ID

[Term]
id: EDAM_data:2611
name: ICD identifier
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a disease from the International Classification of Diseases (ICD) database." [http://edamontology.org]
regex: "[A-Z][0-9]+(\.[-[0-9]+])?"
is_a: EDAM_data:1150 ! Disease ID
relationship: is_identifier_of EDAM_data:1622 ! Disease annotation

[Term]
id: EDAM_data:2800
name: Orpha number
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a disease from the Orpha database." [http://edamontology.org]
is_a: EDAM_data:1150 ! Disease ID
relationship: is_identifier_of EDAM_data:1622 ! Disease annotation

[Term]
id: EDAM_data:2651
name: Disease ID (PharmGKB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org]
regex: "PA[0-9]+"
is_a: EDAM_data:1150 ! Disease ID
is_a: EDAM_data:2649 ! PharmGKB ID


[Term]
id: EDAM_data:2383
name: EGA accession
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the EGA database." [http://edamontology.org]
is_a: EDAM_data:2382 ! Genotype experiment ID

[Term]
id: EDAM_data:2342
name: Pathway or network name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a biological pathway or network." [http://edamontology.org]
is_a: EDAM_data:1082 ! Pathway or network identifier

[Term]
id: EDAM_data:2365
name: Pathway or network accession
namespace: identifier
subset: identifiers
subset: data
def: "A persistent, unique identifier of a biological pathway or network (typically a database entry)." [http://edamontology.org]
is_a: EDAM_data:1082 ! Pathway or network identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:2637
name: cPath ID
namespace: identifier
subset: identifiers
subset: data
def: "A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database." [http://edamontology.org]
comment: These identifiers are unique within the cPath database, however, they are not stable between releases.
regex: "[0-9]+"
is_a: EDAM_data:2109 ! Identifier (hybrid)
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:2659
name: Pathway ID (SMPDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the Small Molecule Pathway Database (SMPDB)." [http://edamontology.org]
regex: "SMP[0-9]{5}"
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:2837
name: Pathway ID (BioSystems)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the BioSystems pathway database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:2650
name: Pathway ID (PharmGKB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)." [http://edamontology.org]
regex: "PA[0-9]+"
is_a: EDAM_data:2365 ! Pathway or network accession
is_a: EDAM_data:2649 ! PharmGKB ID

[Term]
id: EDAM_data:2345
name: Pathway ID (ConsensusPathDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the ConsensusPathDB pathway database." [http://edamontology.org]
is_a: EDAM_data:2917 ! ConsensusPathDB identifier
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:2343
name: Pathway ID (KEGG)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the KEGG pathway database." [http://edamontology.org]
synonym: "KEGG pathway ID" EXACT [http://edamontology.org]
regex: "[a-zA-Z_0-9]{2,3}[0-9]{5}"
is_a: EDAM_data:2365 ! Pathway or network accession
is_a: EDAM_data:1154 ! KEGG object identifier

[Term]
id: EDAM_data:2344
name: Pathway ID (NCI-Nature)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a pathway from the NCI-Nature pathway database." [http://edamontology.org]
regex: "[a-zA-Z_0-9]+"
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:1155
name: Pathway ID (reactome)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the Reactome database." [http://edamontology.org]
synonym: "Reactome ID" EXACT [http://edamontology.org]
regex: "REACT_[0-9]+(\.[0-9]+)?"
is_a: EDAM_data:2365 ! Pathway or network accession

[Term]
id: EDAM_data:1156
name: Pathway ID (aMAZE)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the aMAZE database." [http://edamontology.org]
synonym: "aMAZE ID" EXACT [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:1082 ! Pathway or network identifier

[Term]
id: EDAM_data:1157
name: Pathway ID (BioCyc)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an pathway from the BioCyc biological pathways database." [http://edamontology.org]
synonym: "BioCyc pathway ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2365 ! Pathway or network accession
is_a: EDAM_data:2104 ! BioCyc ID


[Term]
id: EDAM_data:1158
name: Pathway ID (INOH)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the INOH database." [http://edamontology.org]
synonym: "INOH identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:1159
name: Pathway ID (PATIKA)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the PATIKA database." [http://edamontology.org]
synonym: "PATIKA ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2365 ! Pathway or network accession

[Term]
id: EDAM_data:1160
name: Pathway ID (CPDB)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB." [http://edamontology.org]
comment: This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.
synonym: "CPDB ID" EXACT [http://edamontology.org]
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:1161
name: Pathway ID (Panther)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological pathway from the Panther Pathways database." [http://edamontology.org]
synonym: "Panther Pathways ID" EXACT [http://edamontology.org]
regex: "PTHR[0-9]{5}"
is_a: EDAM_data:2365 ! Pathway or network accession

[Term]
id: EDAM_data:2645
name: Pathway ID (Unipathway)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological pathway from the Unipathway database." [http://edamontology.org]
synonym: "upaid" EXACT [http://edamontology.org]
regex: "UPA[0-9]{5}"
is_a: EDAM_data:2365 ! Pathway or network accession


[Term]
id: EDAM_data:2670
name: Pathway ID (DQCS)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS)." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2365 ! Pathway or network accession

[Term]
id: EDAM_data:2591
name: Brite hierarchy ID
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an entry from the Brite database of biological hierarchies." [http://edamontology.org]
is_a: EDAM_data:2891 ! Biological model accession

[Term]
id: EDAM_data:1162
name: MIRIAM identifier
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a MIRIAM data resource." [http://edamontology.org]
comment: This is the identifier used internally by MIRIAM for a data type.
regex: "MIR:[0-9]{8}"
example: "MIR:00100005"
is_a: EDAM_data:2902 ! Data resource definition accession
relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype

[Term]
id: EDAM_data:1163
name: MIRIAM data type name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a data type from the MIRIAM database." [http://edamontology.org]
is_a: EDAM_data:2253 ! Data resource definition name
relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype

[Term]
id: EDAM_data:2253
name: Data resource definition name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a data type." [http://edamontology.org]
is_a: EDAM_data:1084 ! Data resource definition identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:2902
name: Data resource definition accession
namespace: identifier
subset: identifiers
subset: data
def: "Accession of a data definition (catalogued in a database)." [http://edamontology.org]
is_a: EDAM_data:1084 ! Data resource definition identifier
is_a: EDAM_data:2091 ! Accession


[Term]
id: EDAM_data:1164
name: MIRIAM URI
namespace: identifier
subset: identifiers
subset: data
def: "The URI (URL or URN) of a data entity from the MIRIAM database." [http://edamontology.org]
comment: A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.
example: "urn:miriam:pubmed:16333295" "urn:miriam:obo.go:GO%3A0045202" {note="'urn:miriam:pubmed:16333295' is the MIRIAM URI of the publication about MIRIAM, whereas 'urn:miriam:obo.go:GO%3A0045202' refers to GO"}
is_a: EDAM_data:2902 ! Data resource definition accession
is_a: EDAM_data:1047 ! URI
relationship: is_identifier_of EDAM_data:1664 ! MIRIAM datatype

[Term]
id: EDAM_data:1165
name: MIRIAM data type primary name
namespace: identifier
subset: identifiers
subset: data
def: "The primary name of a data type from the MIRIAM database." [http://edamontology.org]
comment: The primary name of a MIRIAM data type is taken from a controlled vocabulary.
example: "UniProt" "Enzyme Nomenclature" {note="A protein entity has the data type 'UniProt', an enzyme has the type 'Enzyme Nomenclature' etc."}
is_a: EDAM_data:1163 ! MIRIAM data type name

[Term]
id: EDAM_data:1166
name: MIRIAM data type synonymous name
namespace: identifier
subset: identifiers
subset: data
def: "A synonymous name of a data type from the MIRIAM database." [http://edamontology.org]
comment: A synonymous name for a MIRIAM data type taken from a controlled vocabulary.
is_a: EDAM_data:1163 ! MIRIAM data type name


[Term]
id: EDAM_data:2106
name: Reaction ID (BioCyc)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological reaction from the BioCyc reactions database." [http://edamontology.org]
is_a: EDAM_data:2108 ! Reaction ID
is_a: EDAM_data:2104 ! BioCyc ID
relationship: has_topic EDAM_topic:0613 ! Peptides and amino acids


[Term]
id: EDAM_data:2309
name: Reaction ID (SABIO-RK)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological reaction from the SABIO-RK reactions database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2108 ! Reaction ID


[Term]
id: EDAM_data:2648
name: Reaction kinetics ID (SABIO-RK)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2309 ! Reaction ID (SABIO-RK)

[Term]
id: EDAM_data:2608
name: Reaction ID (KEGG)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of a biological reaction from the KEGG reactions database." [http://edamontology.org]
regex: "R[0-9]+"
is_a: EDAM_data:2108 ! Reaction ID
is_a: EDAM_data:1154 ! KEGG object identifier

[Term]
id: EDAM_data:2641
name: Reaction ID (MACie)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an enzyme reaction mechanism from the MACie database." [http://edamontology.org]
synonym: "MACie entry number" EXACT [http://edamontology.org]
regex: "M[0-9]{4}"
is_a: EDAM_data:2108 ! Reaction ID

[Term]
id: EDAM_data:2644
name: Reaction ID (Rhea)
namespace: identifier
subset: identifiers
subset: data
def: "Identifier of an enzyme-catalysed reaction from the Rhea database." [http://edamontology.org]
regex: "[0-9]{5}"
is_a: EDAM_data:2108 ! Reaction ID

[Term]
id: EDAM_data:1167
name: Taverna workflow ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a Taverna workflow." [http://edamontology.org]
is_a: EDAM_data:1083 ! Workflow ID


[Term]
id: EDAM_data:1170
name: Biological model name
namespace: identifier
subset: identifiers
subset: data
def: "Name of a biological (mathematical) model." [http://edamontology.org]
is_a: EDAM_data:1085 ! Biological model identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:1171
name: BioModel ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the BioModel database." [http://edamontology.org]
regex: "(BIOMD|MODEL)[0-9]{10}"
is_a: EDAM_data:2891 ! Biological model accession

[Term]
id: EDAM_data:2669
name: ModelDB ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of an entry from the ModelDB database." [http://edamontology.org]
regex: "[0-9]+"
is_a: EDAM_data:2891 ! Biological model accession


[Term]
id: EDAM_data:2339
name: Ontology concept name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a concept in an ontology." [http://edamontology.org]
is_a: EDAM_data:3025 ! Ontology concept identifier
is_a: EDAM_data:2099 ! Name


[Term]
id: EDAM_data:1175
name: BioPax concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the BioPax ontology." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1176
name: GO concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from The Gene Ontology." [http://edamontology.org]
synonym: "GO concept identifier" EXACT [http://edamontology.org]
regex: "[0-9]{7}" "GO:[0-9]{7}"
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1177
name: MeSH concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the MeSH vocabulary." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1178
name: HGNC concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the HGNC controlled vocabulary." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1179
name: NCBI taxonomy ID
namespace: identifier
subset: identifiers
subset: data
def: "A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database." [http://edamontology.org]
regex: "[1-9][0-9]{0,8}"
example: "9662" "3483" "182682"
synonym: "NCBI taxonomy identifier" EXACT [http://edamontology.org]
synonym: "NCBI tax ID" EXACT [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1180
name: Plant Ontology concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the Plant Ontology (PO)." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1181
name: UMLS concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the UMLS vocabulary." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1182
name: FMA concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from Foundational Model of Anatomy." [http://edamontology.org]
comment: Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
regex: "FMA:[0-9]+"
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1183
name: EMAP concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the EMAP mouse ontology." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1184
name: ChEBI concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the ChEBI ontology." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1185
name: MGED concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the MGED ontology." [http://edamontology.org]
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:1186
name: myGrid concept ID
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a concept from the myGrid ontology." [http://edamontology.org]
comment: The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
is_a: EDAM_data:1087 ! Ontology concept ID

[Term]
id: EDAM_data:2705
name: GO concept ID (cellular compartment)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a 'cellular compartment' concept from the Gene Ontology." [http://edamontology.org]
synonym: "GO concept identifier (cellular compartment)" EXACT [http://edamontology.org]
regex: "[0-9]{7}" "GO:[0-9]{7}"
is_a: EDAM_data:1176 ! GO concept ID


[Term]
id: EDAM_data:2582
name: GO concept ID (biological process)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a 'biological process' concept from the the Gene Ontology." [http://edamontology.org]
regex: "[0-9]{7}" "GO:[0-9]{7}"
is_a: EDAM_data:1176 ! GO concept ID

[Term]
id: EDAM_data:2583
name: GO concept ID (molecular function)
namespace: identifier
subset: identifiers
subset: data
def: "An identifier of a 'molecular function' concept from the the Gene Ontology." [http://edamontology.org]
regex: "[0-9]{7}" "GO:[0-9]{7}"
is_a: EDAM_data:1176 ! GO concept ID

[Term]
id: EDAM_data:2581
name: GO concept name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a concept from the GO ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2339 ! Ontology concept name

[Term]
id: EDAM_data:3026
name: GO concept name (biological process)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a concept for a biological process from the GO ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2339 ! Ontology concept name

[Term]
id: EDAM_data:3027
name: GO concept name (molecular function)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a concept for a molecular function from the GO ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2339 ! Ontology concept name

[Term]
id: EDAM_data:2584
name: GO concept name (cellular component)
namespace: identifier
subset: identifiers
subset: data
def: "The name of a concept for a cellular component from the GO ontology." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_data:2339 ! Ontology concept name




! Different biological types of signature are listed below. Bioinformatics types (motif, profile, HMM etc) are given elsewhere

[Term]
id: EDAM_data:1187
name: PubMed ID
namespace: identifier
subset: identifiers
subset: data
def: "PubMed unique identifier of an article." [http://edamontology.org]
synonym: "PMID" EXACT [http://edamontology.org]
regex: "[1-9][0-9]{0,8}"
example: "4963447"
is_a: EDAM_data:1088 ! Article ID

[Term]
id: EDAM_data:1188
name: Digital Object Identifier
namespace: identifier
subset: identifiers
subset: data
def: "Digital Object Identifier (DOI) of a published article." [http://edamontology.org]
regex: "(doi\:)?[0-9]{2}\.[0-9]{4}/.*"
is_a: EDAM_data:1088 ! Article ID

[Term]
id: EDAM_data:1189
name: Medline UI
namespace: identifier
subset: identifiers
subset: data
def: "Medline UI (unique identifier) of an article." [http://edamontology.org]
comment: The use of Medline UI has been replaced by the PubMed unique identifier.
synonym: "Medline unique identifier" EXACT [http://edamontology.org]
is_a: EDAM_data:1088 ! Article ID


[Term]
id: EDAM_data:2634
name: ISBN
namespace: identifier
subset: identifiers
subset: data
def: "The International Standard Book Number (ISBN) is for identifying printed books." [http://edamontology.org]
regex: "(ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X)"
is_a: EDAM_data:2633 ! Book ID

[Term]
id: EDAM_data:2374
name: Spot serial number
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database." [http://edamontology.org]
is_a: EDAM_data:2373 ! Spot ID


[Term]
id: EDAM_data:2375
name: Spot ID (HSC-2DPAGE)
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database." [http://edamontology.org]
is_a: EDAM_data:2373 ! Spot ID

[Term]
id: EDAM_data:2588
name: BlotBase blot ID
namespace: identifier
subset: identifiers
subset: data
def: "Unique identifier of a blot from a Northern Blot from the BlotBase database." [http://edamontology.org]
is_a: EDAM_data:2587 ! Blot ID

[Term]
id: EDAM_data:1046
name: Strain name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [http://edamontology.org]
is_a: EDAM_data:2909 ! Organism name
is_a: EDAM_data:2379 ! Strain identifier


[Term]
id: EDAM_data:2778
name: CCAP strain number
namespace: identifier
subset: identifiers
subset: data
def: "The number of a strain of algae and protozoa from the CCAP database." [http://edamontology.org]
is_a: EDAM_data:2912 ! Strain accession

[Term]
id: EDAM_data:2316
name: Cell line name
namespace: identifier
subset: identifiers
subset: data
def: "The name of a cell line." [http://edamontology.org]
is_a: EDAM_data:1046 ! Strain name

[Term]
id: EDAM_data:2112
name: FlyBase primary identifier
namespace: identifier
subset: identifiers
subset: data
def: "Primary identifier of an object from the FlyBase database." [http://edamontology.org]
is_a: EDAM_data:1089 ! FlyBase ID


[Term]
id: EDAM_data:2174
name: FlyBase secondary identifier
namespace: identifier
subset: identifiers
subset: data
def: "Secondary identifier of an object from the FlyBase database." [http://edamontology.org]
comment: Secondary identifier are used to handle entries that were merged with or split from other entries in the database.
is_a: EDAM_data:1089 ! FlyBase ID


[Term]
id: EDAM_data:1091
name: WormBase name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an object from the WormBase database, usually a human-readable name." [http://edamontology.org]
is_a: EDAM_data:2113 ! WormBase identifier
is_a: EDAM_data:2099 ! Name

[Term]
id: EDAM_data:1092
name: WormBase class
namespace: identifier
subset: identifiers
subset: data
def: "Class of an object from the WormBase database." [http://edamontology.org]
comment: A WormBase class describes the type of object such as 'sequence' or 'protein'.
is_a: EDAM_data:2113 ! WormBase identifier


[Term]
id: EDAM_data:2254
name: OBO file format name
namespace: identifier
subset: identifiers
subset: data
def: "Name of an OBO file format such as OBO-XML, plain and so on." [http://edamontology.org]
is_a: EDAM_data:2129 ! File format name



!
! Format
!

[Term]
id: EDAM_format:2350
name: Format (typed)
namespace: format
subset: formats
def: "A broad class of format distinguished by the scientific nature of the data that is identified." [http://edamontology.org]
comment: This concept exists only to assist EDAM maintenance and navigation in graphical browsers.  It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.
is_a: EDAM_format:1915 ! Format


[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:2331
name: HTML
namespace: format
subset: formats
def: "HTML format." [http://edamontology.org]
synonym: "Hypertext Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/HTML]
synonym: "HTML" EXACT [http://filext.com/file-extension/HTML] {note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."}
synonym: "HTM" EXACT [http://filext.com/file-extension/HTM] {note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."}
is_a: EDAM_format:1915 ! Format
relationship: is_format_of EDAM_data:2048 ! Report

[Term]
id: EDAM_format:2332
name: XML
namespace: format
subset: formats
def: "eXtensible Markup Language (XML) format." [http://edamontology.org]
comment: Data in XML format can be serialised into text, or binary format.
synonym: "Extensible Markup Language" EXACT [http://edamontology.org, http://filext.com/file-extension/XML]
synonym: "XML" EXACT [http://filext.com/file-extension/XML] {note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."}
is_a: EDAM_format:1915 ! Format

[Term]
id: EDAM_format:2333
name: Binary format
namespace: format
subset: formats
def: "Binary format." [http://edamontology.org]
comment: Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.
is_a: EDAM_format:1915 ! Format


[Term]
id: EDAM_format:2376
name: RDF
namespace: format
subset: formats
def: "Resource Description Framework (RDF) format." [http://edamontology.org]
comment: Data in RDF format can be serialised into XML, textual, or binary format.
is_a: EDAM_format:1915 ! Format

[Term]
id: EDAM_format:2921
name: Sequence variation annotation format
namespace: format
subset: formats
def: "Format of sequence variation annotation." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0918 ! Nucleic acid features (variation)


[Term]
id: EDAM_format:2919
name: Sequence annotation track format
namespace: format
subset: formats
def: "Format of a sequence annotation track." [http://edamontology.org]
is_a: EDAM_format:1920 ! Sequence feature annotation format
relationship: is_format_of EDAM_data:3002 ! Sequence annotation track

[Term]
id: EDAM_format:2352
name: BioXSD
namespace: format
subset: formats
def: "BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more)." [http://edamontology.org]
synonym: "BioXSD XML format" EXACT [http://edamontology.org]
xref: http://bioxsd.org {documentation=true}
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:1919 ! Sequence record format
is_a: EDAM_format:1920 ! Sequence feature annotation format
is_a: EDAM_format:2555 ! Alignment format (XML)
is_a: EDAM_format:2332 ! XML
relationship: is_format_of EDAM_data:2044 ! Sequence
relationship: is_format_of EDAM_data:1255 ! Feature record
relationship: is_format_of EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_format:2848
name: Bibliographic reference format
namespace: format
subset: formats
def: "Format of a bibliographic reference." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0970 ! Bibliographic reference
relationship: is_format_of EDAM_data:2849 ! Abstract


[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_format:1918
name: Atomic data format
namespace: format
subset: formats
def: "Data format for an individual atom." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_format:1475 ! PDB database entry format

[Term]
id: EDAM_format:1919
name: Sequence record format
namespace: format
subset: formats
def: "Data format for a molecular sequence record." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0849 ! Sequence record

[Term]
id: EDAM_format:1920
name: Sequence feature annotation format
namespace: format
subset: formats
def: "Data format for molecular sequence feature information." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1255 ! Feature record

[Term]
id: EDAM_format:1921
name: Alignment format
namespace: format
subset: formats
def: "Data format for molecular sequence alignment information." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0863 ! Sequence alignment

[Term]
id: EDAM_format:2920
name: Alignment format (pair only)
namespace: format
subset: formats
def: "Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences." [http://edamontology.org]
is_a: EDAM_format:1921 ! Alignment format
relationship: is_format_of EDAM_data:1381 ! Sequence alignment (pair)

[Term]
id: EDAM_format:2006
name: Phylogenetic tree format
namespace: format
subset: formats
def: "Data format for a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0872 ! Phylogenetic tree

[Term]
id: EDAM_format:2033
name: Tertiary structure format
namespace: format
subset: formats
def: "Data format for a molecular tertiary structure." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)

[Term]
id: EDAM_format:3167
name: Experiment annotation format
namespace: format
subset: formats
def: "Data format for annotation on a laboratory experiment." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)


[Term]
id: EDAM_format:2034
name: Biological model format
namespace: format
subset: formats
def: "Data format for a biological model." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0950 ! Biological model

[Term]
id: EDAM_format:2014
name: Sequence-profile alignment format
namespace: format
subset: formats
def: "Data format for a sequence-profile alignment." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0869 ! Sequence-profile alignment

[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:2017
name: Amino acid index format
namespace: format
subset: formats
def: "Data format for an amino acid index." [http://edamontology.org]
is_a: EDAM_format:3033 ! Matrix format
relationship: is_format_of EDAM_data:1501 ! Amino acid index

[Term]
id: EDAM_format:2020
name: Article format
namespace: format
subset: formats
def: "Data format for a full-text scientific article." [http://edamontology.org]
synonym: "Literature format" EXACT [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0971 ! Article

[Term]
id: EDAM_format:2021
name: Text mining report format
namespace: format
subset: formats
def: "Data format for an abstract (report) from text mining." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0972 ! Text mining report

[Term]
id: EDAM_format:2027
name: Enzyme kinetics report format
namespace: format
subset: formats
def: "Data format for reports on enzyme kinetics." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:2024 ! Enzyme kinetics data

[Term]
id: EDAM_format:2030
name: Small molecule report format
namespace: format
subset: formats
def: "Format of a report on a chemical compound." [http://edamontology.org]
synonym: "Chemical compound annotation format" EXACT [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0962 ! Small molecule annotation

[Term]
id: EDAM_format:2031
name: Gene annotation format
namespace: format
subset: formats
def: "Format of a report on a particular locus, gene, gene system or groups of genes." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0916 ! Gene annotation

[Term]
id: EDAM_format:2032
name: Workflow format
namespace: format
subset: formats
def: "Format of a workflow." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:2972 ! Workflow

[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_format:2036
name: Phylogenetic character data format
namespace: format
subset: formats
def: "Format of raw (unplotted) phylogenetic data." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0871 ! Phylogenetic character data

[Term]
id: EDAM_format:3097 {since=beta13}
name: Protein domain classification format
namespace: format
subset: formats
def: "Format of data concerning the classification of the sequences and/or structures of protein structural domain(s)." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0900 ! Protein domain classification


[Term]
id: EDAM_format:3098 {since=beta13}
name: Raw SCOP domain classification format
namespace: format
subset: formats
def: "Format of raw SCOP domain classification data files." [http://edamontology.org]
comment: These are the parsable data files provided by SCOP.
is_a: EDAM_format:3097 ! Protein domain classification format

[Term]
id: EDAM_format:3099 {since=beta13}
name: Raw CATH domain classification format
namespace: format
subset: formats
def: "Format of raw CATH domain classification data files." [http://edamontology.org]
comment: These are the parsable data files provided by CATH.
is_a: EDAM_format:3097 ! Protein domain classification format

[Term]
id: EDAM_format:3100 {since=beta13}
name: CATH domain report format
namespace: format
subset: formats
def: "Format of summary of domain classification information for a CATH domain." [http://edamontology.org]
comment: The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
is_a: EDAM_format:3097 ! Protein domain classification format


[Term]
id: EDAM_format:2045
name: Electron microscopy model format
namespace: format
subset: formats
def: "Annotation format for electron microscopy models." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2350 ! Format (typed)


[Term]
id: EDAM_format:2049
name: Phylogenetic tree report (tree distances) format
namespace: format
subset: formats
def: "Format for phylogenetic tree distance data." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1442 ! Phylogenetic tree report (tree distances)

[Term]
id: EDAM_format:2051
name: Polymorphism report format
namespace: format
subset: formats
def: "Format for sequence polymorphism data." [http://edamontology.org]
is_obsolete: true !{since=1.0}
! is_a: EDAM_format:2350 ! Format (typed)
! relationship: is_format_of EDAM_data:2885 ! Nucleic acid features (polymorphism annotation)

[Term]
id: EDAM_format:2052
name: Protein family report format
namespace: format
subset: formats
def: "Format for reports on a protein family." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0907 ! Protein family

[Term]
id: EDAM_format:2054
name: Protein interaction format
namespace: format
subset: formats
def: "Format for protein interaction data." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0906 ! Protein interaction


[Term]
id: EDAM_format:2055
name: Sequence assembly format
namespace: format
subset: formats
def: "Format for sequence assembly data." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0925 ! Sequence assembly

[Term]
id: EDAM_format:2056
name: Microarray experiment data format
namespace: format
subset: formats
def: "Format for microarray experimental data." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0931 ! Experiment annotation (microarray)

[Term]
id: EDAM_format:2058
name: Gene expression report format
namespace: format
subset: formats
def: "Format for a report on gene expression." [http://edamontology.org]
is_a: EDAM_format:2031 ! Gene annotation format
relationship: is_format_of EDAM_data:3111 ! Processed microarray data

[Term]
id: EDAM_format:2059
name: Genotype and phenotype annotation format
namespace: format
subset: formats
def: "Format of a report on genotype / phenotype information." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0920 ! Genotype/phenotype annotation

[Term]
id: EDAM_format:2060
name: Map format
namespace: format
subset: formats
def: "Format of a map of (typically one) molecular sequence annotated with features." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1274 ! Map

[Term]
id: EDAM_format:2061
name: Nucleic acid features (primers) format
namespace: format
subset: formats
def: "Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0922 ! Nucleic acid features (primers)

[Term]
id: EDAM_format:2062
name: Protein report format
namespace: format
subset: formats
def: "Format of a report of general information about a specific protein." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0896 ! Protein report

[Term]
id: EDAM_format:3033 {since=beta13}
name: Matrix format
namespace: format
subset: formats
def: "Format of a matrix (array) of numerical values." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:2082 ! Matrix

[Term]
id: EDAM_format:2064
name: 3D-1D scoring matrix format
namespace: format
subset: formats
def: "Format of a matrix of 3D-1D scores (amino acid environment probabilities)." [http://edamontology.org]
is_a: EDAM_format:3033 ! Matrix format
relationship: is_format_of EDAM_data:1499 ! 3D-1D scoring matrix

[Term]
id: EDAM_format:2065
name: Protein structure report (quality evaluation) format
namespace: format
subset: formats
def: "Format of a report on the quality of a protein three-dimensional model." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1539 ! Protein structural quality report


[Term]
id: EDAM_format:2066
name: Database hits (sequence) format
namespace: format
subset: formats
def: "Format of a report on sequence hits and associated data from searching a sequence database." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0857 ! Database hits (sequence)

[Term]
id: EDAM_format:2067
name: Sequence distance matrix format
namespace: format
subset: formats
def: "Format of a matrix of genetic distances between molecular sequences." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0870 ! Sequence distance matrix

[Term]
id: EDAM_format:2068
name: Sequence motif format
namespace: format
subset: formats
def: "Format of a sequence motif." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1353 ! Sequence motif

[Term]
id: EDAM_format:2069
name: Sequence profile format
namespace: format
subset: formats
def: "Format of a sequence profile." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1354 ! Sequence profile

[Term]
id: EDAM_format:2074
name: Dirichlet distribution format
namespace: format
subset: formats
def: "Data format of a dirichlet distribution." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1347 ! Dirichlet distribution

[Term]
id: EDAM_format:2075
name: HMM emission and transition counts format
namespace: format
subset: formats
def: "Data format for the emission and transition counts of a hidden Markov model." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1348 ! HMM emission and transition counts

[Term]
id: EDAM_format:2077
name: Protein secondary structure format
namespace: format
subset: formats
def: "Format for secondary structure (predicted or real) of a protein molecule." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0876 ! Protein features (secondary structure)

[Term]
id: EDAM_format:2076
name: RNA secondary structure format
namespace: format
subset: formats
def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record

[Term]
id: EDAM_format:2078
name: Sequence range format
namespace: format
subset: formats
def: "Format used to specify range(s) of sequence positions." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1017 ! Sequence range

[Term]
id: EDAM_format:2155
name: Sequence features (repeats) format
namespace: format
subset: formats
def: "Format used for map of repeats in molecular (typically nucleotide) sequences." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1299 ! Sequence features (repeats)

[Term]
id: EDAM_format:2158
name: Nucleic acid features (restriction sites) format
namespace: format
subset: formats
def: "Format used for report on restriction enzyme recognition sites in nucleotide sequences." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1305 ! Nucleic acid features (restriction sites)

[Term]
id: EDAM_format:2159
name: Gene features (coding region) format
namespace: format
subset: formats
def: "Format used for report on coding regions in nucleotide sequences." [http://edamontology.org]
is_a: EDAM_format:2031 ! Gene annotation format
relationship: is_format_of EDAM_data:1313 ! Nucleic acid features (coding sequence)

[Term]
id: EDAM_format:2170
name: Sequence cluster format
namespace: format
subset: formats
def: "Format used for clusters of molecular sequences." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:1235 ! Sequence cluster

[Term]
id: EDAM_format:2195
name: Ontology format
namespace: format
subset: formats
def: "Format used for ontologies." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0582 ! Ontology

[Term]
id: EDAM_format:2210
name: Strain data format
namespace: format
subset: formats
def: "Format of a report on organism strain data / cell line." [http://edamontology.org]
is_obsolete: true !{since=1.0}
! is_a: EDAM_format:2350 ! Format (typed)
! relationship: is_format_of EDAM_data:0963 ! Cell line annotation

[Term]
id: EDAM_format:2542
name: Protein features (domains) format
namespace: format
subset: formats
def: "Format of a report on protein features (domain composition)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2350 ! Format (typed)

[Term]
id: EDAM_format:2571
name: Raw sequence format
namespace: format
subset: formats
def: "Format of a raw molecular sequence (i.e. the alphabet used)." [http://edamontology.org]
synonym: "Symbol sequence" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:0848 ! Raw sequence

[Term]
id: EDAM_format:1734
name: PubMed citation
namespace: format
subset: formats
def: "Format of bibliographic reference as used by the PubMed database." [http://edamontology.org]
is_a: EDAM_format:2848 ! Bibliographic reference format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1735
name: Medline Display Format
namespace: format
subset: formats
def: "Format for abstracts of scientific articles from the Medline database." [http://edamontology.org]
comment: Bibliographic reference information including citation information is included
xref: Moby:PubMed-MEDLINE
is_a: EDAM_format:2848 ! Bibliographic reference format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1736
name: CiteXplore-core
namespace: format
subset: formats
def: "CiteXplore 'core' citation format including title, journal, authors and abstract." [http://edamontology.org]
is_a: EDAM_format:2848 ! Bibliographic reference format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1737
name: CiteXplore-all
namespace: format
subset: formats
def: "CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references." [http://edamontology.org]
is_a: EDAM_format:2848 ! Bibliographic reference 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_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:2552
name: Sequence record format (XML)
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:2203
name: Sequence record lite format
namespace: format
subset: formats
def: "Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment." [http://edamontology.org]
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:2043 ! Sequence record lite

[Term]
id: EDAM_format:2202
name: Sequence record full format
namespace: format
subset: formats
def: "Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database." [http://edamontology.org]
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:2201 ! Sequence record full


[Term]
id: EDAM_format:2057
name: Sequence trace format
namespace: format
subset: formats
def: "Format for sequence trace data (i.e. including base call information)." [http://edamontology.org]
is_a: EDAM_format:1919 ! Sequence record format
relationship: is_format_of EDAM_data:0924 ! Sequence trace

[Term]
id: EDAM_format:1923
name: acedb
namespace: format
subset: formats
def: "ACEDB sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)


[Term]
id: EDAM_format:1924
name: clustal sequence format
namespace: format
subset: formats
def: "Clustalw output format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1982 ! clustal

[Term]
id: EDAM_format:1925
name: codata
namespace: format
subset: formats
def: "Codata entry format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1928
name: experiment
namespace: format
subset: formats
def: "Staden experiment file format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1934
name: fitch
namespace: format
subset: formats
def: "Fitch program format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1935
name: gcg
namespace: format
subset: formats
def: "GCG sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1938
name: GFF2-seq
namespace: format
subset: formats
def: "GFF feature file format with sequence in the header." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1974 ! GFF2


[Term]
id: EDAM_format:1939
name: GFF3-seq
namespace: format
subset: formats
def: "GFF3 feature file format with sequence." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1975 ! GFF3


[Term]
id: EDAM_format:1941
name: hennig86
namespace: format
subset: formats
def: "Hennig86 output sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1942
name: ig
namespace: format
subset: formats
def: "Intelligenetics sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1943
name: igstrict
namespace: format
subset: formats
def: "Intelligenetics sequence format (strict version)." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1944
name: jackknifer
namespace: format
subset: formats
def: "Jackknifer interleaved and non-interleaved sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1945
name: mase
namespace: format
subset: formats
def: "Mase program sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1946
name: mega-seq
namespace: format
subset: formats
def: "Mega interleaved and non-interleaved sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1947
name: msf
namespace: format
subset: formats
def: "GCG MSF (multiple sequence file) file format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1949
name: nexus-seq
namespace: format
subset: formats
def: "Nexus/paup interleaved sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1950
name: pdbatom
namespace: format
subset: formats
def: "PDB sequence format (ATOM lines)." [http://edamontology.org]
comment: pdb format in EMBOSS.
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1951
name: pdbatomnuc
namespace: format
subset: formats
def: "PDB nucleotide sequence format (ATOM lines)." [http://edamontology.org]
comment: pdbnuc format in EMBOSS.
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1952
name: pdbseqresnuc
namespace: format
subset: formats
def: "PDB nucleotide sequence format (SEQRES lines)." [http://edamontology.org]
comment: pdbnucseq format in EMBOSS.
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1953
name: pdbseqres
namespace: format
subset: formats
def: "PDB sequence format (SEQRES lines)." [http://edamontology.org]
comment: pdbseq format in EMBOSS.
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1955
name: phylip sequence format
namespace: format
subset: formats
def: "Phylip interleaved sequence format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1997 ! phylip

[Term]
id: EDAM_format:1956
name: phylipnon sequence format
namespace: format
subset: formats
def: "Phylip non-interleaved sequence format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1998 ! phylipnon


[Term]
id: EDAM_format:1957
name: raw
namespace: format
subset: formats
def: "Raw sequence format with no non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

! For now, identical to genpept
[Term]
id: EDAM_format:1958
name: refseqp
namespace: format
subset: formats
def: "Refseq protein entry sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1959
name: selex sequence format
namespace: format
subset: formats
def: "Selex sequence format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2000 ! selex


[Term]
id: EDAM_format:1960
name: Staden format
namespace: format
subset: formats
def: "Staden suite sequence format." [http://edamontology.org]
xref: http://www.bio.net/bionet/mm/bio-soft/1991-October/003063.html {documentation=true}
xref: http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#staden {documentation=true}
is_a: EDAM_format:2551 ! Sequence record format (text)
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:1962
name: strider
namespace: format
subset: formats
def: "DNA strider output sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1964
name: text
namespace: format
subset: formats
def: "Plain text sequence format (essentially unformatted)." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1965
name: treecon sequence format
namespace: format
subset: formats
def: "Treecon output sequence format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2005 ! treecon-seq


[Term]
id: EDAM_format:1966
name: asn1 sequence format
namespace: format
subset: formats
def: "NCBI ASN.1 sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1969
name: debug-seq
namespace: format
subset: formats
def: "EMBOSS debugging trace sequence format of full internal data content." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1970
name: jackknifernon
namespace: format
subset: formats
def: "Jackknifer output sequence non-interleaved format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1971
name: meganon sequence format
namespace: format
subset: formats
def: "Mega non-interleaved output sequence format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1992 ! meganon

[Term]
id: EDAM_format:1973
name: nexusnon
namespace: format
subset: formats
def: "Nexus/paup non-interleaved sequence format." [http://edamontology.org]
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1967
name: das
namespace: format
subset: formats
def: "DAS sequence (XML) format (any type)." [http://edamontology.org]
synonym: "das sequence format" EXACT [http://edamontology.org]
is_a: EDAM_format:2552 ! Sequence record format (XML)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1968
name: dasdna
namespace: format
subset: formats
def: "DAS sequence (XML) format (nucleotide-only)." [http://edamontology.org]
comment: The use of this format is deprecated.
is_a: EDAM_format:2552 ! Sequence record format (XML)
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:2546
name: FASTA-like
namespace: format
subset: formats
def: "A format resembling FASTA format." [http://edamontology.org]
comment: This concept may be used for the many non-standard FASTA-like formats.
is_a: EDAM_format:2203 ! Sequence record lite format


[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:2310
name: FASTA-HTML
namespace: format
subset: formats
def: "FASTA format wrapped in HTML elements." [http://edamontology.org]
is_a: EDAM_format:2546 ! FASTA-like
is_a: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1929
name: FASTA format
namespace: format
subset: formats
def: "FASTA format including NCBI-style IDs." [http://edamontology.org] ! Is it different from 1972?
synonym: "FASTA" EXACT [http://edamontology.org]
synonym: "FASTA sequence format" EXACT [http://edamontology.org]
is_a: EDAM_format:2200 ! FASTA-like (text)
is_a: EDAM_format:2554 ! Alignment format (text)

[Term]
id: EDAM_format:1926
name: dbid
namespace: format
subset: formats
def: "Fasta format variant with database name before ID." [http://edamontology.org]
is_a: EDAM_format:2200 ! FASTA-like (text)

[Term]
id: EDAM_format:1940
name: giFASTA format
namespace: format
subset: formats
def: "FASTA sequence format including NCBI-style GIs." [http://edamontology.org]
is_a: EDAM_format:2200 ! FASTA-like (text)

[Term]
id: EDAM_format:1954
name: Pearson format
namespace: format
subset: formats
def: "Plain old FASTA sequence format (unspecified format for IDs)." [http://edamontology.org]
is_a: EDAM_format:2200 ! FASTA-like (text)

[Term]
id: EDAM_format:1972
name: NCBI format
namespace: format
subset: formats
def: "NCBI FASTA sequence format with NCBI-style IDs." [http://edamontology.org]
comment: There are several variants of this.
is_a: EDAM_format:2200 ! FASTA-like (text)

[Term]
id: EDAM_format:2543
name: EMBL-like format
namespace: format
subset: formats
def: "A format resembling EMBL entry (plain text) format." [http://edamontology.org]
comment: This concept may be used for the many non-standard EMBL-like formats.
is_a: EDAM_format:2202 ! Sequence record full format


[Term]
id: EDAM_format:2559
name: GenBank-like format
namespace: format
subset: formats
def: "A format resembling GenBank entry (plain text) format." [http://edamontology.org]
comment: This concept may be used for the non-standard GenBank-like formats.
is_a: EDAM_format:2202 ! Sequence record full format

[Term]
id: EDAM_format:2547
name: uniprotkb-like format
namespace: format
subset: formats
def: "A sequence format resembling uniprotkb entry format." [http://edamontology.org]
is_a: EDAM_format:2202 ! Sequence record full format
is_a: EDAM_format:2206 ! Sequence feature table format (text)

[Term]
id: EDAM_format:1948
name: nbrf
namespace: format
subset: formats
def: "NBRF/PIR entry sequence format." [http://edamontology.org]
is_a: EDAM_format:2202 ! Sequence record full format
is_a: EDAM_format:2330 ! Textual format

[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:2558
name: EMBL-like (XML)
namespace: format
subset: formats
def: "An XML format resembling EMBL entry format." [http://edamontology.org]
comment: This concept may be used for the any non-standard EMBL-like XML formats.
is_a: EDAM_format:2543 ! EMBL-like format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:2311
name: EMBL-HTML
namespace: format
subset: formats
def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org]
is_a: EDAM_format:2543 ! EMBL-like format
is_a: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1927
name: EMBL format
namespace: format
subset: formats
def: "EMBL entry format." [http://edamontology.org]
synonym: "EMBL sequence format" EXACT [http://edamontology.org]
synonym: "EMBL" EXACT [http://edamontology.org]
is_a: EDAM_format:2181 ! EMBL-like (text)
is_a: EDAM_format:2206 ! Sequence feature table format (text)

[Term]
id: EDAM_format:2186
name: geneseq
namespace: format
subset: formats
def: "Geneseq sequence format." [http://edamontology.org]
is_a: EDAM_format:2181 ! EMBL-like (text)

[Term]
id: EDAM_format:2204
name: EMBL format (XML)
namespace: format
subset: formats
def: "An XML format for EMBL entries." [http://edamontology.org]
comment: This is a placeholder for other more specific concepts. It should not normally be used for annotation.
is_a: EDAM_format:2558 ! EMBL-like (XML)

[Term]
id: EDAM_format:2183
name: EMBLXML
namespace: format
subset: formats
def: "XML format for EMBL entries." [http://edamontology.org]
is_a: EDAM_format:2204 ! EMBL format (XML)


[Term]
id: EDAM_format:2184
name: cdsxml
namespace: format
subset: formats
def: "XML format for EMBL entries." [http://edamontology.org]
is_a: EDAM_format:2204 ! EMBL format (XML)

[Term]
id: EDAM_format:2185
name: insdxml
namespace: format
subset: formats
def: "XML format for EMBL entries." [http://edamontology.org]
is_a: EDAM_format:2204 ! EMBL format (XML)


[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:2532
name: GenBank-HTML
namespace: format
subset: formats
def: "Genbank entry format wrapped in HTML elements." [http://edamontology.org]
is_a: EDAM_format:2559 ! GenBank-like format
is_a: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1936
name: GenBank format
namespace: format
subset: formats
def: "Genbank entry format." [http://edamontology.org]
is_a: EDAM_format:2205 ! GenBank-like format (text)
is_a: EDAM_format:2206 ! Sequence feature table format (text)


! For now, identical to refseqp
[Term]
id: EDAM_format:1937
name: genpept
namespace: format
subset: formats
def: "Genpept protein entry format." [http://edamontology.org]
is_a: EDAM_format:2205 ! GenBank-like format (text)


[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:1963
name: Swiss-Prot format
namespace: format
subset: formats
def: "Swiss-Prot entry sequence format." [http://edamontology.org]
is_a: EDAM_format:2187 ! uniprotkb-like (text)


[Term]
id: EDAM_format:2188
name: uniprot
namespace: format
subset: formats
def: "UniProt entry sequence format." [http://edamontology.org]
is_a: EDAM_format:2187 ! uniprotkb-like (text)

[Term]
id: EDAM_format:2189
name: ipi
namespace: format
subset: formats
def: "ipi sequence format." [http://edamontology.org]
is_a: EDAM_format:2187 ! uniprotkb-like (text)


[Term]
id: EDAM_format:1628
name: ABI
namespace: format
subset: formats
def: "A format of raw sequence read data from an Applied Biosystems sequencing machine." [http://edamontology.org]
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2333 ! Binary 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:2545
name: FASTQ-like format
namespace: format
subset: formats
def: "A 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:2057 ! Sequence trace format


[Term]
id: EDAM_format:2572
name: BAM
namespace: format
subset: formats
def: "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data." [http://edamontology.org]
xref: http://samtools.sourceforge.net/SAM-1.3.pdf {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:1921 ! Alignment format
is_a: EDAM_format:2333 ! Binary format

[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_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:1930
name: FASTQ
namespace: format
subset: formats
def: "FASTQ short read format ignoring quality scores." [http://edamontology.org]
is_a: EDAM_format:2182 ! FASTQ-like format (text)

[Term]
id: EDAM_format:1931
name: FASTQ-illumina
namespace: format
subset: formats
def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org]
is_a: EDAM_format:2182 ! FASTQ-like format (text)

[Term]
id: EDAM_format:1932
name: FASTQ-sanger
namespace: format
subset: formats
def: "FASTQ short read format with phred quality." [http://edamontology.org]
is_a: EDAM_format:2182 ! FASTQ-like format (text)

[Term]
id: EDAM_format:1933
name: FASTQ-solexa
namespace: format
subset: formats
def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org]
is_a: EDAM_format:2182 ! FASTQ-like format (text)

[Term]
id: EDAM_format:2548
name: Sequence feature table format
namespace: format
subset: formats
def: "Format for a sequence feature table." [http://edamontology.org]
is_a: EDAM_format:1920 ! Sequence feature annotation format
relationship: is_format_of EDAM_data:1255 ! Feature record

[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: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_format:2553
name: Sequence feature table format (XML)
namespace: format
subset: formats
def: "XML format for a sequence feature table." [http://edamontology.org]
is_a: EDAM_format:2548 ! Sequence feature table format


[Term]
id: EDAM_format:2305
name: GFF
namespace: format
subset: formats
def: "GFF feature format (of indeterminate version)." [http://edamontology.org]
is_a: EDAM_format:2206 ! Sequence feature table format (text)
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1976
name: pir
namespace: format
subset: formats
def: "PIR feature format." [http://edamontology.org]
is_a: EDAM_format:2206 ! Sequence feature table format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1977
name: swiss feature
namespace: format
subset: formats
def: "Swiss-Prot feature format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1963 ! Swiss-Prot format


[Term]
id: EDAM_format:1980
name: EMBL feature
namespace: format
subset: formats
def: "EMBL feature format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1927 ! EMBL format


[Term]
id: EDAM_format:1981
name: GenBank feature
namespace: format
subset: formats
def: "Genbank feature format." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1936 ! GenBank 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:2306
name: GTF
namespace: format
subset: formats
def: "Gene Transfer Format (GTF), a restricted version of GFF." [http://edamontology.org]
xref: http://mblab.wustl.edu/GTF22.html {documentation=true}
xref: http://genome.ucsc.edu/FAQ/FAQformat#format4 {documentation=true}
is_a: EDAM_format:2305 ! GFF


[Term]
id: EDAM_format:1978
name: DASGFF
namespace: format
subset: formats
def: "DAS GFF (XML) feature format." [http://edamontology.org]
synonym: "DASGFF feature" EXACT [http://edamontology.org]
synonym: "das feature" EXACT [http://edamontology.org]
is_a: EDAM_format:2553 ! Sequence feature table format (XML)
is_a: EDAM_format:2332 ! XML

[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:2555
name: Alignment format (XML)
namespace: format
subset: formats
def: "XML format for molecular sequence alignment information." [http://edamontology.org]
is_a: EDAM_format:1921 ! Alignment format

[Term]
id: EDAM_format:1982
name: clustal
namespace: format
subset: formats
def: "Clustalw format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1983
name: debug
namespace: format
subset: formats
def: "EMBOSS alignment format for debugging trace of full internal data content." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1984
name: FASTA-aln
namespace: format
subset: formats
def: "Fasta format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2200 ! FASTA-like (text)

[Term]
id: EDAM_format:2922
name: markx0 variant
namespace: format
subset: formats
def: "Some variant of Pearson MARKX alignment format." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1985
name: markx0
namespace: format
subset: formats
def: "Pearson MARKX0 alignment format." [http://edamontology.org]
is_a: EDAM_format:2922 ! markx0 variant


[Term]
id: EDAM_format:1986
name: markx1
namespace: format
subset: formats
def: "Pearson MARKX1 alignment format." [http://edamontology.org]
is_a: EDAM_format:2922 ! markx0 variant


[Term]
id: EDAM_format:1987
name: markx10
namespace: format
subset: formats
def: "Pearson MARKX10 alignment format." [http://edamontology.org]
is_a: EDAM_format:2922 ! markx0 variant


[Term]
id: EDAM_format:1988
name: markx2
namespace: format
subset: formats
def: "Pearson MARKX2 alignment format." [http://edamontology.org]
is_a: EDAM_format:2922 ! markx0 variant


[Term]
id: EDAM_format:1989
name: markx3
namespace: format
subset: formats
def: "Pearson MARKX3 alignment format." [http://edamontology.org]
is_a: EDAM_format:2922 ! markx0 variant


[Term]
id: EDAM_format:1990
name: match
namespace: format
subset: formats
def: "Alignment format for start and end of matches between sequence pairs." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:2923
name: mega variant
namespace: format
subset: formats
def: "Some variant of Mega format for (typically aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1991
name: mega
namespace: format
subset: formats
def: "Mega format for (typically aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2923 ! mega variant

[Term]
id: EDAM_format:1992
name: meganon
namespace: format
subset: formats
def: "Mega non-interleaved format for (typically aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2923 ! mega variant


[Term]
id: EDAM_format:1993
name: msf alignment format
namespace: format
subset: formats
def: "MSF format for (aligned) sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1947 ! msf

[Term]
id: EDAM_format:1994
name: nexus alignment format
namespace: format
subset: formats
def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1949 ! nexus-seq

[Term]
id: EDAM_format:1995
name: nexusnon alignment format
namespace: format
subset: formats
def: "Nexus/paup non-interleaved format for (aligned) sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:1973 ! nexusnon

[Term]
id: EDAM_format:1996
name: pair
namespace: format
subset: formats
def: "EMBOSS simple sequence pair alignment format." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)

[Term]
id: EDAM_format:2924
name: phylip variant
namespace: format
subset: formats
def: "Some variant of Phylip format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1997
name: phylip
namespace: format
subset: formats
def: "Phylip format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2924 ! phylip variant

[Term]
id: EDAM_format:1998
name: phylipnon
namespace: format
subset: formats
def: "Phylip non-interleaved format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2924 ! phylip variant


[Term]
id: EDAM_format:1999
name: score
namespace: format
subset: formats
def: "Alignment format for score values for pairs of sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2000
name: selex
namespace: format
subset: formats
def: "SELEX format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2001
name: simple
namespace: format
subset: formats
def: "EMBOSS simple multiple alignment format." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2002
name: srs
namespace: format
subset: formats
def: "Simple multiple sequence (alignment) format for SRS." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2003
name: srspair
namespace: format
subset: formats
def: "Simple sequence pair (alignment) format for SRS." [http://edamontology.org]
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2004
name: tcoffee
namespace: format
subset: formats
def: "TCOFFEE program alignment format." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2005
name: treecon-seq
namespace: format
subset: formats
def: "Treecon format for (aligned) sequences." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2551 ! Sequence record format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1391
name: hmmer-aln
namespace: format
subset: formats
def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1392
name: dialign
namespace: format

subset: formats
def: "Multiple sequences aligned by DIALIGN package." [http://edamontology.org]
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1393
name: daf
namespace: format
subset: formats
def: "EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family." [http://edamontology.org]
comment: The format is clustal-like and includes annotation of domain family classification information.
is_a: EDAM_format:2554 ! Alignment format (text)
is_a: EDAM_format:2330 ! Textual 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:2557
name: Phylogenetic tree format (XML)
namespace: format
subset: formats
def: "XML format for a phylogenetic tree." [http://edamontology.org]
is_a: EDAM_format:2006 ! Phylogenetic tree format


[Term]
id: EDAM_format:1435
name: phylip tree
namespace: format
subset: formats
def: "Phylogenetic tree data format used by the PHYLIP program." [http://edamontology.org]
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1425
name: Phylip tree raw
namespace: format
subset: formats
def: "Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted." [http://edamontology.org]
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1424
name: Clustalw dendrogram
namespace: format
subset: formats
def: "Dendrogram (tree file) format generated by Clustalw." [http://edamontology.org]
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1436
name: treebase
namespace: format
subset: formats
def: "The format of an entry from the TreeBASE database of phylogenetic data." [http://edamontology.org]
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1437
name: treefam
namespace: format
subset: formats
def: "The format of an entry from the TreeFam database of phylogenetic data." [http://edamontology.org]
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1910
name: newick
namespace: format
subset: formats
def: "Phylogenetic tree Newick (text) format." [http://edamontology.org]
xref: Moby:Newick_Text
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1911
name: treecon
namespace: format
subset: formats
def: "Phylogenetic tree TreeCon (text) format." [http://edamontology.org]
xref: Moby:TreeCon
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1912
name: nexus
namespace: format
subset: formats
def: "Phylogenetic tree Nexus (text) format." [http://edamontology.org]
xref: Moby:Nexus_Text
is_a: EDAM_format:2556 ! Phylogenetic tree format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1475
name: PDB database entry format
namespace: format
subset: formats
def: "Format of an entry (or part of an entry) from the PDB database." [http://edamontology.org]
synonym: "PDB entry" EXACT [http://edamontology.org]
is_a: EDAM_format:2033 ! Tertiary structure format

[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_format:1478
name: PDBML
namespace: format
subset: formats
def: "Entry format of PDB database in PDBML (XML) format." [http://edamontology.org]
is_a: EDAM_format:1475 ! PDB database entry format
is_a: EDAM_format:2332 ! XML


[Term]
id: EDAM_format:2013
name: Biological pathway or network format
namespace: format
subset: formats
def: "Data format for a biological pathway or network." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:2600 ! Pathway or network


[Term]
id: EDAM_format:3166
name: Biological pathway or network report format
namespace: format
subset: formats
def: "Data format for a report of information derived from a biological pathway or network." [http://edamontology.org]
is_a: EDAM_format:2350 ! Format (typed)
relationship: is_format_of EDAM_data:2984 ! Pathway or network report



[Term]
id: EDAM_format:2585
name: SBML
namespace: format
subset: formats
def: "Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation." [http://edamontology.org]
xref: http://sbml.org {documentation=true}
is_a: EDAM_format:2034 ! Biological model format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3155 {since=1.0}
name: SBRML
namespace: format
subset: formats
def: "Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models." [http://edamontology.org]
xref: http://www.comp-sys-bio.org/tiki-index.php?page=SBRML {documentation=true}
is_a: EDAM_format:3166 ! Biological pathway or network report format
is_a: EDAM_format:2332 ! XML


[Term]
id: EDAM_format:3156 {since=1.0}
name: BioPAX
namespace: format
subset: formats
def: "BioPAX is an exchange format for pathway data, with its data model defined in OWL." [http://edamontology.org]
xref: http://www.biopax.org {documentation=true}
is_a: EDAM_format:2013 ! Biological pathway or network format
is_a: EDAM_format:2197 ! OWL

[Term]
id: EDAM_format:3157 {since=1.0}
name: EBI Application Result XML
namespace: format
subset: formats
def: "EBI Application Result XML is a format returned by sequence similarity search Web services at EBI." [http://edamontology.org]
xref: http://www.ebi.ac.uk/schema/ApplicationResult.xsd {documentation=true}
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2920 ! Alignment format (pair only)
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3158 {since=1.0}
name: PSI MI XML (MIF)
namespace: format
subset: formats
def: "XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI." [http://edamontology.org]
xref: http://psidev.sourceforge.net/mi/xml/doc/user {documentation=true}
is_a: EDAM_format:2054 ! Protein interaction format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3159 {since=1.0}
name: phyloXML
namespace: format
subset: formats
def: "phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data." [http://edamontology.org]
xref: http://www.phyloxml.org {documentation=true}
is_a: EDAM_format:2557 ! Phylogenetic tree format (XML)
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3160 {since=1.0}
name: NeXML
namespace: format
subset: formats
def: "NeXML is a standardised XML format for rich phyloinformatic data." [http://edamontology.org]
xref: http://www.nexml.org {documentation=true}
is_a: EDAM_format:2557 ! Phylogenetic tree format (XML) ! And more
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3161 {since=1.0}
name: MAGE-ML
namespace: format
subset: formats
def: "MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org]
xref: http://www.mged.org/Workgroups/MAGE/mage-ml.html {documentation=true}
is_a: EDAM_format:2058 ! Gene expression report format
is_a: EDAM_format:2056 ! Microarray experiment data format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:3162 {since=1.0}
name: MAGE-TAB
namespace: format
subset: formats
def: "MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED)." [http://edamontology.org]
xref: http://www.mged.org/mage-tab {documentation=true}
is_a: EDAM_format:2058 ! Gene expression report format
is_a: EDAM_format:2056 ! Microarray experiment data format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:3163 {since=1.0}
name: GCDML
namespace: format
subset: formats
def: "GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC)." [http://edamontology.org]
xref: http://gcdml.gensc.org {documentation=true}
is_a: EDAM_format:3167 ! Experiment annotation format
is_a: EDAM_format:2332 ! XML
relationship: is_format_of EDAM_data:3165 ! Experiment annotation (sequencing)

[Term]
id: EDAM_format:3164 {since=1.0}
name: GTrack
namespace: format
subset: formats
def: "GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG)." [http://edamontology.org]
xref: http://www.gtrack.no {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1666
name: BioModel mathematical model format
namespace: format
subset: formats
def: "Format of mathematical models from the BioModel database." [http://edamontology.org]
comment: Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1647
name: KEGG PATHWAY entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1648
name: MetaCyc entry format
namespace: format
subset: formats
def: "The format of an entry from the MetaCyc metabolic pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1649
name: HumanCyc entry format
namespace: format
subset: formats
def: "The format of a report from the HumanCyc metabolic pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1650
name: INOH entry format
namespace: format
subset: formats
def: "The format of an entry from the INOH signal transduction pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML



[Term]
id: EDAM_format:1651
name: PATIKA entry format
namespace: format
subset: formats
def: "The format of an entry from the PATIKA biological pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1652
name: Reactome entry format
namespace: format
subset: formats
def: "The format of an entry from the reactome biological pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1653
name: aMAZE entry format
namespace: format
subset: formats
def: "The format of an entry from the aMAZE biological pathways and molecular interactions database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1654
name: CPDB entry format
namespace: format
subset: formats
def: "The format of an entry from the CPDB database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1655
name: Panther Pathways entry format
namespace: format
subset: formats
def: "The format of an entry from the Panther Pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2341
name: NCI-Nature pathway entry format
namespace: format
subset: formats
def: "The format of an entry from the NCI-Nature pathways database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2015
name: Sequence-profile alignment (HMM) format
namespace: format
subset: formats
def: "Data format for a sequence-HMM profile alignment." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2014 ! Sequence-profile alignment format


[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: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: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: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: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: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:1697
name: KEGG LIGAND entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG LIGAND chemical database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1698
name: KEGG COMPOUND entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG COMPOUND database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1699
name: KEGG PLANT entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG PLANT database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1700
name: KEGG GLYCAN entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG GLYCAN database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1706
name: KEGG DRUG entry format
namespace: format
subset: formats
def: "The format of an entry from the KEGG DRUG database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1701
name: PubChem entry format
namespace: format
subset: formats
def: "The format of an entry from PubChem." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1702
name: ChemSpider entry format
namespace: format
subset: formats
def: "The format of an entry from a database of chemical structures and property predictions." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1703
name: ChEBI entry format
namespace: format
subset: formats
def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [http://edamontology.org]
comment: ChEBI includes an ontological classification defining relations between entities or classes of entities.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1704
name: MSDchem ligand dictionary entry format
namespace: format
subset: formats
def: "The format of an entry from the MSDchem ligand dictionary." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[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:1808
name: GeneIlluminator gene report format
namespace: format
subset: formats
def: "Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service." [http://edamontology.org]
comment: This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.
xref: Moby:GI_Gene
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1809
name: BacMap gene card format
namespace: format
subset: formats
def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [http://edamontology.org]
xref: Moby:BacMapGeneCard
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1810
name: ColiCard report format
namespace: format
subset: formats
def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [http://edamontology.org]
xref: Moby:ColiCard
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2328
name: PseudoCAP gene report format
namespace: format
subset: formats
def: "Format of a report on a gene from the PseudoCAP database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2329
name: GeneCards gene report format
namespace: format
subset: formats
def: "Format of a report on a gene from the GeneCards database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1603
name: Ensembl gene report format
namespace: format
subset: formats
def: "Entry format of Ensembl genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1604
name: DictyBase gene report format
namespace: format
subset: formats
def: "Entry format of DictyBase genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1605
name: CGD gene report format
namespace: format
subset: formats
def: "Entry format of Candida Genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1606
name: DragonDB gene report format
namespace: format
subset: formats
def: "Entry format of DragonDB genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1607
name: EcoCyc gene report format
namespace: format
subset: formats
def: "Entry format of EcoCyc genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1608
name: FlyBase gene report format
namespace: format
subset: formats
def: "Entry format of FlyBase genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1609
name: Gramene gene report format
namespace: format
subset: formats
def: "Entry format of Gramene genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1610
name: KEGG GENES gene report format
namespace: format
subset: formats
def: "Entry format of KEGG GENES genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1611
name: MaizeGDB gene report format
namespace: format
subset: formats
def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1612
name: MGD gene report format
namespace: format
subset: formats
def: "Entry format of the Mouse Genome Database (MGD)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1613
name: RGD gene report format
namespace: format
subset: formats
def: "Entry format of the Rat Genome Database (RGD)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1614
name: SGD gene report format
namespace: format
subset: formats
def: "Entry format of the Saccharomyces Genome Database (SGD)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1615
name: GeneDB gene report format
namespace: format
subset: formats
def: "Entry format of the Sanger GeneDB genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1616
name: TAIR gene report format
namespace: format
subset: formats
def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1617
name: WormBase gene report format
namespace: format
subset: formats
def: "Entry format of the WormBase genomes database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1618
name: ZFIN gene report format
namespace: format
subset: formats
def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1619
name: TIGR gene report format
namespace: format
subset: formats
def: "Entry format of the TIGR genome database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1782
name: NCBI gene report format
namespace: format
subset: formats
def: "Entry (gene) format of the NCBI database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1665
name: Taverna workflow format
namespace: format
subset: formats
def: "Format of Taverna workflows." [http://edamontology.org]
is_a: EDAM_format:2032 ! Workflow format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:1196
name: smiles
namespace: format
subset: formats
def: "Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation." [http://edamontology.org]
is_a: EDAM_format:2035 ! Chemical formula format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1197
name: inchi
namespace: format
subset: formats
def: "Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation." [http://edamontology.org]
is_a: EDAM_format:2035 ! Chemical formula format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1198
name: mf
namespace: format
subset: formats
def: "Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound." [http://edamontology.org]
comment: The general MF query format consists of a series of valid atomic symbols, with an optional number or range.
is_a: EDAM_format:2035 ! Chemical formula format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1199
name: inchikey
namespace: format
subset: formats
def: "The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound." [http://edamontology.org]
comment: An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.
is_a: EDAM_format:2035 ! Chemical formula format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1200
name: smarts
namespace: format
subset: formats
def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [http://edamontology.org]
is_a: EDAM_format:1196 ! smiles

[Term]
id: EDAM_format:2037
name: Phylogenetic continuous quantitative character format
namespace: format
subset: formats
def: "Format of phylogenetic continuous quantitative character data." [http://edamontology.org]
is_a: EDAM_format:2036 ! Phylogenetic character data format
relationship: is_format_of EDAM_data:1426 ! Phylogenetic continuous quantitative data

[Term]
id: EDAM_format:1431
name: Phylogenetic property values format
namespace: format
subset: formats
def: "Format of phylogenetic property data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2036 ! Phylogenetic character data format


[Term]
id: EDAM_format:2038
name: Phylogenetic discrete states format
namespace: format
subset: formats
def: "Format of phylogenetic discrete states data." [http://edamontology.org]
is_a: EDAM_format:2036 ! Phylogenetic character data format
relationship: is_format_of EDAM_data:1427 ! Phylogenetic discrete data

[Term]
id: EDAM_format:2039
name: Phylogenetic tree report (cliques) format
namespace: format
subset: formats
def: "Format of phylogenetic cliques data." [http://edamontology.org]
is_a: EDAM_format:2036 ! Phylogenetic character data format
relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques


[Term]
id: EDAM_format:2040
name: Phylogenetic tree report (invariants) format
namespace: format
subset: formats
def: "Format of phylogenetic invariants data." [http://edamontology.org]
is_a: EDAM_format:2036 ! Phylogenetic character data format
relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants

[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:2243
name: phylip property values
namespace: format
subset: formats
def: "PHYLIP file format for phylogenetic property data." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2036 ! Phylogenetic character data 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:1645
name: EMDB entry format
namespace: format
subset: formats
def: "Format of an entry from the Electron Microscopy DataBase (EMDB)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[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:1620
name: dbSNP polymorphism report format
namespace: format
subset: formats
def: "Entry format for the dbSNP database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1570
name: InterPro entry format
namespace: format
subset: formats
def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [http://edamontology.org]
comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1571
name: InterPro entry abstract format
namespace: format
subset: formats
def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [http://edamontology.org]
comment: References are included and a functional inference is made where possible.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1572
name: Gene3D entry format
namespace: format
subset: formats
def: "Entry format for the Gene3D protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1573
name: PIRSF entry format
namespace: format
subset: formats
def: "Entry format for the PIRSF protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1574
name: PRINTS entry format
namespace: format
subset: formats
def: "Entry format for the PRINTS protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1575
name: Panther Families and HMMs entry format
namespace: format
subset: formats
def: "Entry format for the Panther library of protein families and subfamilies." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1576
name: Pfam entry format
namespace: format
subset: formats
def: "Entry format for the Pfam protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1577
name: SMART entry format
namespace: format
subset: formats
def: "Entry format for the SMART protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1578
name: Superfamily entry format
namespace: format
subset: formats
def: "Entry format for the Superfamily protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1579
name: TIGRFam entry format
namespace: format
subset: formats
def: "Entry format for the TIGRFam protein secondary database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1580
name: ProDom entry format
namespace: format
subset: formats
def: "Entry format for the ProDom protein domain classification database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1581
name: FSSP entry format
namespace: format
subset: formats
def: "Entry format for the FSSP database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1568
name: BIND entry format
namespace: format
subset: formats
def: "Entry format for the BIND database of protein interaction." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1569
name: IntAct entry format
namespace: format
subset: formats
def: "Entry format for the IntAct database of protein interaction." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:2560
name: STRING entry format
namespace: format
subset: formats
def: "Entry format for the STRING database of protein interaction." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:2303
name: STRING entry format (HTML)
namespace: format
subset: formats
def: "Entry format (HTML) for the STRING database of protein interaction." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2304
name: STRING entry format (XML)
namespace: format
subset: formats
def: "Entry format (XML) for the STRING database of protein interaction." [http://edamontology.org]
is_a: EDAM_format:2054 ! Protein interaction format
is_a: EDAM_format:2332 ! XML


[Term]
id: EDAM_format:2561
name: Sequence assembly format (text)
namespace: format
subset: formats
def: "Text format for sequence assembly data." [http://edamontology.org]
is_a: EDAM_format:2055 ! Sequence assembly 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:1631
name: exp
namespace: format
subset: formats
def: "Sequence assembly project file EXP format." [http://edamontology.org]
is_a: EDAM_format:2561 ! Sequence assembly format (text)
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1632
name: SCF
namespace: format
subset: formats
def: "Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata." [http://edamontology.org]
xref: http://staden.sourceforge.net/manual/formats_unix_2.html {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2333 ! Binary 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:1640
name: ArrayExpress entry format
namespace: format
subset: formats
def: "Entry format for the ArrayExpress microarrays database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[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: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: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: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:1623
name: OMIM entry format
namespace: format
subset: formats
def: "Format of an entry from the OMIM database of genotypes and phenotypes." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1624
name: HGVbase entry format
namespace: format
subset: formats
def: "Format of a record from the HGVbase database of genotypes and phenotypes." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1625
name: HIVDB entry format
namespace: format
subset: formats
def: "Format of a record from the HIVDB database of genotypes and phenotypes." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1626
name: KEGG DISEASE entry format
namespace: format
subset: formats
def: "Format of an entry from the KEGG DISEASE database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[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: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:2063
name: Protein report (enzyme) format
namespace: format
subset: formats
def: "Format of a report of general information about a specific enzyme." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2350 ! Format (typed)

[Term]
id: EDAM_format:1511
name: IntEnz enzyme report format
namespace: format
subset: formats
def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)." [http://edamontology.org]
comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1512
name: BRENDA enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the BRENDA enzyme database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2322
name: BioCyc enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the BioCyc enzyme database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:2323
name: ENZYME enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1513
name: KEGG REACTION enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the KEGG REACTION database of biochemical reactions." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1514
name: KEGG ENZYME enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the KEGG ENZYME database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1515
name: REBASE proto enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the proto section of the REBASE enzyme database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:1516
name: REBASE withrefm enzyme report format
namespace: format
subset: formats
def: "Format of an entry from the withrefm section of the REBASE enzyme database." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[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: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:1341
name: InterPro hits format
namespace: format
subset: formats
def: "Results format for searches of the InterPro database." [http://edamontology.org]
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1342
name: InterPro protein view report format
namespace: format
subset: formats
def: "Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries." [http://edamontology.org]
comment: The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.
is_a: EDAM_format:1341 ! InterPro hits format


[Term]
id: EDAM_format:1343
name: InterPro match table format
namespace: format
subset: formats
def: "Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry." [http://edamontology.org]
comment: The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.
is_a: EDAM_format:1341 ! InterPro hits format

[Term]
id: EDAM_format:1332
name: FASTA search results format
namespace: format
subset: formats
def: "Format of results of a sequence database search using FASTA." [http://edamontology.org]
comment: This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)
is_a: EDAM_format:2066 ! Database hits (sequence) format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1333
name: BLAST results
namespace: format
subset: formats
def: "Format of results of a sequence database search using some variant of BLAST." [http://edamontology.org]
comment: This includes score data, alignment data and summary table.
is_a: EDAM_format:2066 ! Database hits (sequence) 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: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: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: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:2072
name: Hidden Markov model format
namespace: format
subset: formats
def: "Format of a hidden Markov model." [http://edamontology.org]
is_a: EDAM_format:2069 ! Sequence profile format
relationship: is_format_of EDAM_data:1364 ! Hidden Markov model

[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: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: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_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: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_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_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: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: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:2171
name: Sequence cluster format (protein)
namespace: format
subset: formats
def: "Format used for clusters of protein sequences." [http://edamontology.org]
is_a: EDAM_format:2170 ! Sequence cluster format

[Term]
id: EDAM_format:2172
name: Sequence cluster format (nucleic acid)
namespace: format
subset: formats
def: "Format used for clusters of nucleotide sequences." [http://edamontology.org]
is_a: EDAM_format:2170 ! Sequence cluster format

[Term]
id: EDAM_format:1247
name: COG sequence cluster format
namespace: format
subset: formats
def: "Format of an entry from the COG database of clusters of (related) protein sequences." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML


[Term]
id: EDAM_format:2175
name: Gene cluster format
namespace: format
subset: formats
! alt_id: EDAM_format:2918
def: "Format used for clusters of genes." [http://edamontology.org]
is_obsolete: true !{since=beta13}
consider: EDAM_format:2172 ! Sequence cluster format (nucleic acid)


[Term]
id: EDAM_format:1228
name: UniGene entry format
namespace: format
subset: formats
def: "Format of an entry from UniGene." [http://edamontology.org]
comment: A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[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:2196
name: OBO format
namespace: format
subset: formats
def: "OBO ontology format." [http://edamontology.org]
is_a: EDAM_format:2195 ! Ontology format

[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: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_format:2550
name: OBO-XML
namespace: format
subset: formats
def: "OBO ontology XML format." [http://edamontology.org]
is_a: EDAM_format:2196 ! OBO format
is_a: EDAM_format:2332 ! XML

[Term]
id: EDAM_format:2211
name: CIP strain data format
namespace: format
subset: formats
def: "Format for a report of strain data as used for CIP database entries." [http://edamontology.org]
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1760
name: CATH chain report format
namespace: format
subset: formats
def: "Format of CATH domain classification information for a polypeptide chain." [http://edamontology.org]
comment: The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1761
name: CATH PDB report format
namespace: format
subset: formats
def: "Format of CATH domain classification information for a protein PDB file." [http://edamontology.org]
comment: The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:1563
name: SMART domain assignment report format
namespace: format
subset: formats
def: "Format of SMART domain assignment data." [http://edamontology.org]
comment: The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.
is_obsolete: true !{since=beta12orEarlier}
consider: EDAM_format:2331 ! HTML

[Term]
id: EDAM_format:3000
name: AB1
namespace: format
subset: formats
def: "AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence." [http://www.fileinfo.com/extension/ab1, http://edamontology.org]
comment: AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).
is_a: EDAM_format:2333 ! Binary format
is_a: EDAM_format:2057 ! Sequence trace format

[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:3004
name: bigBed
namespace: format
subset: formats
def: "bigBed format for large sequence annotation tracks, similar to textual BED format." [http://edamontology.org]
xref: http://genome.ucsc.edu/FAQ/FAQformat#format1.5 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2333 ! Binary 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:3006
name: bigWig
namespace: format
subset: formats
def: "bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format." [http://edamontology.org]
xref: http://genome.ucsc.edu/FAQ/FAQformat#format6.1 {documentation=true}
is_a: EDAM_format:2919 ! Sequence annotation track format
is_a: EDAM_format:2333 ! Binary 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:3009
name: 2bit
namespace: format
subset: formats
def: "2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'." [http://edamontology.org]
xref: http://jcomeau.freeshell.org/www/genome/2bitformat.html {documentation=true}
xref: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/twoBit.h;hb=HEAD {documentation=true}
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2333 ! Binary format

[Term]
id: EDAM_format:3010
name: .nib
namespace: format
subset: formats
def: ".nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'." [http://edamontology.org]
xref: http://genome.ucsc.edu/FAQ/FAQformat#format8 {documentation=true}
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2333 ! Binary format

[Term]
id: EDAM_format:2094
name: pure
namespace: format
subset: formats
def: "Alphabet for molecular sequence with possible unknown positions but without non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2095
name: unpure
namespace: format
subset: formats
def: "Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2096
name: unambiguous sequence
namespace: format
subset: formats
def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters." [http://edamontology.org]

is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2566
name: completely unambiguous
namespace: format
subset: formats
def: "Alphabet for a molecular sequence without any unknown positions or ambiguity characters." [http://edamontology.org]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:2097
name: ambiguous
namespace: format
subset: formats
def: "Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters." [http://edamontology.org]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1207
name: nucleotide
namespace: format
subset: formats
def: "Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org]
comment: Non-sequence characters may be used for example for gaps.
synonym: "Nucleotide sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format

[Term]
id: EDAM_format:1208
name: protein
namespace: format
subset: formats
def: "Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org]
comment: Non-sequence characters may be used for gaps and translation stop.
synonym: "Amino acid sequence" EXACT [http://edamontology.org]
synonym: "Amino acid sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence]
is_a: EDAM_format:2571 ! Raw sequence format
is_a: EDAM_format:2330 ! Textual format


[Term]
id: EDAM_format:1206
name: unambiguous pure
namespace: format
subset: formats
def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2094 ! pure
is_a: EDAM_format:2096 ! unambiguous sequence

[Term]
id: EDAM_format:2567
name: completely unambiguous pure
namespace: format
subset: formats
def: "Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2094 ! pure
is_a: EDAM_format:2566 ! completely unambiguous


[Term]
id: EDAM_format:1209
name: consensus
namespace: format
subset: formats
def: "Alphabet for the consensus of two or more molecular sequences." [http://edamontology.org]
is_a: EDAM_format:2097 ! ambiguous
is_a: EDAM_format:2095 ! unpure

[Term]
id: EDAM_format:1210
name: pure nucleotide
namespace: format
subset: formats
def: "Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2094 ! pure
is_a: EDAM_format:1207 ! nucleotide

[Term]
id: EDAM_format:1211
name: unambiguous pure nucleotide
namespace: format
subset: formats
def: "Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters ." [http://edamontology.org]
is_a: EDAM_format:1207 ! nucleotide
is_a: EDAM_format:1206 ! unambiguous pure


[Term]
id: EDAM_format:2568
name: completely unambiguous pure nucleotide
namespace: format
subset: formats
def: "Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters ." [http://edamontology.org]
is_a: EDAM_format:1207 ! nucleotide
is_a: EDAM_format:2567 ! completely unambiguous pure


[Term]
id: EDAM_format:1212
name: dna
namespace: format
subset: formats
def: "Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org]
synonym: "DNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence]
is_a: EDAM_format:1207 ! nucleotide

[Term]
id: EDAM_format:1213
name: rna
namespace: format
subset: formats
def: "Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters." [http://edamontology.org]
synonym: "RNA sequence" RELATED [ttp://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence]
is_a: EDAM_format:1207 ! nucleotide

[Term]
id: EDAM_format:1214
name: unambiguous pure dna
namespace: format
subset: formats
def: "Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:1206 ! unambiguous pure
is_a: EDAM_format:1212 ! dna

[Term]
id: EDAM_format:2569
name: completely unambiguous pure dna
namespace: format
subset: formats
def: "Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2567 ! completely unambiguous pure
is_a: EDAM_format:1212 ! dna

[Term]
id: EDAM_format:1215
name: pure dna
namespace: format
subset: formats
def: "Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:1210 ! pure nucleotide
is_a: EDAM_format:1212 ! dna

[Term]
id: EDAM_format:1216
name: unambiguous pure rna sequence
namespace: format
subset: formats
def: "Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:1206 ! unambiguous pure
is_a: EDAM_format:1213 ! rna

[Term]
id: EDAM_format:2570
name: completely unambiguous pure rna sequence
namespace: format
subset: formats
def: "Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2567 ! completely unambiguous pure
is_a: EDAM_format:1213 ! rna

[Term]
id: EDAM_format:1217
name: pure rna
namespace: format
subset: formats
def: "Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:1210 ! pure nucleotide
is_a: EDAM_format:1213 ! rna

[Term]
id: EDAM_format:1218
name: unambiguous pure protein
namespace: format
subset: formats
def: "Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:1206 ! unambiguous pure
is_a: EDAM_format:1208 ! protein

[Term]
id: EDAM_format:2607
name: completely unambiguous pure protein
namespace: format
subset: formats
def: "Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2567 ! completely unambiguous pure
is_a: EDAM_format:1208 ! protein

[Term]
id: EDAM_format:1219
name: pure protein
namespace: format
subset: formats
def: "Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters." [http://edamontology.org]
is_a: EDAM_format:2094 ! pure
is_a: EDAM_format:1208 ! protein

[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:todo if desired (but then we could include 100 ucsc db tables) At least, this one is used also in IGV (for importing genome cytobands)
! name: Cytoband format
! namespace: format
! subset: formats
! def: "Cytoband format for chromosome cytobands." [http://edamontology.org]
! comment: Reflects a UCSC Browser DB table.
! xref: http://www.broadinstitute.org/software/igv/Cytoband {documentation=true}


[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

[Term]
id: EDAM_format:3017
name: SRF
namespace: format
subset: formats
def: "Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive." [http://edamontology.org, http://srf.sourceforge.net/ShortSequenceFormatDec18th_v_1_3.htm]
xref: http://srf.sourceforge.net/ {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2333 ! Binary format

[Term]
id: EDAM_format:3018
name: ZTR
namespace: format
subset: formats
def: "ZTR format for storing chromatogram data from DNA sequencing instruments." [http://staden.sourceforge.net/manual/formats_unix_12.html, http://edamontology.org]
xref: http://staden.sourceforge.net/manual/formats_unix_12.html {documentation=true}
is_a: EDAM_format:2057 ! Sequence trace format
is_a: EDAM_format:2333 ! Binary format

[Term]
id: EDAM_format:3019
name: GVF
namespace: format
subset: formats
def: "Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation." [http://edamontology.org]
xref: http://sequenceontology.org/gvf.html {documentation=true}
is_a: EDAM_format:1975 ! GFF3
! is_format_of (1255, Sequence feature annotation) is defined in parent (+ here has special tags for a particular class of seqfeatures: variation (indels,polymphs,structvar))

[Term]
id: EDAM_format:3020
name: BCF
namespace: format
subset: formats
def: "BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)." [http://edamontology.org]
xref: http://samtools.sourceforge.net/mpileup.shtml {documentation=true, note="BCF described on this site"}
is_a: EDAM_format:2921 ! Sequence variation annotation format
is_a: EDAM_format:2333 ! Binary format

