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Class: GeneToGoTermAssociation

Description: A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates.

Aliases: functional association

classDiagram class GeneToGoTermAssociation FunctionalAssociation <|-- GeneToGoTermAssociation GeneToGoTermAssociation : adjusted_p_value GeneToGoTermAssociation : agent_type GeneToGoTermAssociation --|> AgentTypeEnum : agent_type GeneToGoTermAssociation : aggregator_knowledge_source GeneToGoTermAssociation : category GeneToGoTermAssociation : deprecated GeneToGoTermAssociation : description GeneToGoTermAssociation : elevate_to_prediction GeneToGoTermAssociation : evidence_count GeneToGoTermAssociation : has_attribute GeneToGoTermAssociation --|> Attribute : has_attribute GeneToGoTermAssociation : has_confidence_score GeneToGoTermAssociation : has_evidence GeneToGoTermAssociation --|> InformationContentEntity : has_evidence GeneToGoTermAssociation : has_evidence_of_type GeneToGoTermAssociation --|> EvidenceType : has_evidence_of_type GeneToGoTermAssociation : has_supporting_studies GeneToGoTermAssociation --|> Study : has_supporting_studies GeneToGoTermAssociation : id GeneToGoTermAssociation : iri GeneToGoTermAssociation : knowledge_level GeneToGoTermAssociation --|> KnowledgeLevelEnum : knowledge_level GeneToGoTermAssociation : knowledge_source GeneToGoTermAssociation : name GeneToGoTermAssociation : negated GeneToGoTermAssociation : object GeneToGoTermAssociation --|> OntologyClass : object GeneToGoTermAssociation : object_category GeneToGoTermAssociation --|> OntologyClass : object_category GeneToGoTermAssociation : object_category_closure GeneToGoTermAssociation --|> OntologyClass : object_category_closure GeneToGoTermAssociation : object_closure GeneToGoTermAssociation : object_feature_name GeneToGoTermAssociation : object_label_closure GeneToGoTermAssociation : object_namespace GeneToGoTermAssociation : original_object GeneToGoTermAssociation : original_predicate GeneToGoTermAssociation : original_subject GeneToGoTermAssociation : p_value GeneToGoTermAssociation : predicate GeneToGoTermAssociation : primary_knowledge_source GeneToGoTermAssociation : publications GeneToGoTermAssociation --|> Publication : publications GeneToGoTermAssociation : qualifier GeneToGoTermAssociation : qualifiers GeneToGoTermAssociation --|> OntologyClass : qualifiers GeneToGoTermAssociation : retrieval_source_ids GeneToGoTermAssociation --|> RetrievalSource : retrieval_source_ids GeneToGoTermAssociation : semmed_agreement_count GeneToGoTermAssociation : sources GeneToGoTermAssociation --|> RetrievalSource : sources GeneToGoTermAssociation : subject GeneToGoTermAssociation --|> Gene : subject GeneToGoTermAssociation : subject_category GeneToGoTermAssociation --|> OntologyClass : subject_category GeneToGoTermAssociation : subject_category_closure GeneToGoTermAssociation --|> OntologyClass : subject_category_closure GeneToGoTermAssociation : subject_closure GeneToGoTermAssociation : subject_feature_name GeneToGoTermAssociation : subject_label_closure GeneToGoTermAssociation : subject_namespace GeneToGoTermAssociation : supporting_text GeneToGoTermAssociation : timepoint GeneToGoTermAssociation : type GeneToGoTermAssociation : update_date

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject:
gene, product or macromolecular complex that has the function associated with the GO term
1
Gene		 Association ZFIN:ZDB-GENE-050417-357
predicate:
Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats 		1
Uriorcurie		 Association
object:
class describing the activity, process or localization of the gene product 		1
OntologyClass		 Association GO:0016301
negated:
if set to true, then the association is negated i.e. is not true 		0..1
Boolean		 Association
qualifier:
grouping slot for all qualifiers on an edge. useful for testing compliance with association classes 		0..1
String		 Association
qualifiers:
connects an association to qualifiers that modify or qualify the meaning of that association 		*
OntologyClass		 Association
publications:
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. 		*
Publication		 Association
sources:
A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org). 		*
RetrievalSource		 Association
has_evidence_of_type:
Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology. 		*
EvidenceType		 Association
has_evidence:
Connects an association to detailed information providing supporting evidence. 		*
InformationContentEntity		 Association
knowledge_source:
An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property. 		0..1
String		 Association
primary_knowledge_source:
The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to capture non-primary sources. 		0..1
String		 Association
aggregator_knowledge_source:
An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form. 		*
String		 Association
knowledge_level:
Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true. 		1
KnowledgeLevelEnum		 Association knowledge_assertion, prediction, statistical_association
agent_type:
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information. 		1
AgentTypeEnum		 Association manual_agent, automated_agent, computational_model, text_mining_agent
timepoint:
a point in time 		0..1
TimeType		 Association
original_subject:
used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
original_predicate:
used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
Uriorcurie		 Association
original_object:
used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
subject_feature_name:
Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene 		0..1
String		 Association
object_feature_name:
Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease 		0..1
String		 Association
subject_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Gene
object_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Disease
subject_closure:
Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association
object_closure:
Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['MONDO:0000167', 'MONDO:0005395']
subject_category_closure:
Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Gene", "biolink:NamedThing']
object_category_closure:
Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Disease", "biolink:NamedThing']
subject_namespace:
Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association NCBIGene
object_namespace:
Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association MONDO
subject_label_closure:
Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['BRCA1']
object_label_closure:
Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association breast cancer, cancer
retrieval_source_ids:
A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. 		*
RetrievalSource		 Association
p_value:
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. 		0..1
Float		 Association
adjusted_p_value:
The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<. 		0..1
Float		 Association
supporting_text:
The segment of text from a document that supports the mined assertion. 		*
String		 Association Here, we report two new cases of rivaroxaban-induced hepatitis.
has_supporting_studies:
Studies that produced information used as evidence to generate the knowledge expressed in an Association. 		*
Study		 Association
update_date:
date on which an entity was updated. This can be applied to nodes or edges 		0..1
Date		 Association
has_confidence_score:
connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about. 		0..1
Float		 Association
elevate_to_prediction:
A boolean flag indicating whether a clinical trial finding should be elevated to a prediction. 		0..1
Boolean		 Association
evidence_count:
The number of evidence instances that are connected to an association. 		0..1
Integer		 Association
semmed_agreement_count:
The number of times this concept has been asserted in the SemMedDB literature database. 		0..1
Integer		 Association
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing} 		*
Uriorcurie		 Entity
type:
rdf:type of biolink:Association should be fixed at rdf:Statement 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

Example values

Slot Name Value
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None
GeneToGoTermAssociation None

LinkML Source

name: gene to go term association
description: A functional association between a gene (or gene product or macromolecular
  complex) and a Gene Ontology (GO) term describing the molecular function, biological
  process, or cellular component in which it participates.
examples:
- object:
    subject: NCBIGene:25595
    predicate: biolink:active_in
    object: GO:0015630
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: manual_validation_of_automated_agent
- object:
    subject: NCBIGene:20502
    predicate: biolink:acts_upstream_of
    object: GO:0042403
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: manual_validation_of_automated_agent
- object:
    subject: NCBIGene:308911
    predicate: biolink:acts_upstream_of_negative_effect
    object: GO:1903450
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: manual_validation_of_automated_agent
- object:
    subject: NCBIGene:101148
    predicate: biolink:acts_upstream_of_or_within
    object: GO:0031669
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: manual_validation_of_automated_agent
- object:
    subject: NCBIGene:18072
    predicate: biolink:acts_upstream_of_or_within_positive_effect
    object: GO:0006915
    category: biolink:GeneToGoTermAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
    publications:
    - PMID:17573818
- object:
    subject: NCBIGene:12168
    predicate: biolink:colocalizes_with
    object: GO:0005901
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: automated_agent
- object:
    subject: NCBIGene:303888
    predicate: biolink:contributes_to
    object: GO:0160270
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: manual_validation_of_automated_agent
- object:
    subject: NCBIGene:12193
    predicate: biolink:enables
    object: GO:0046872
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: automated_agent
- object:
    subject: NCBIGene:258177
    predicate: biolink:located_in
    object: GO:0016020
    category: biolink:GeneToGoTermAssociation
    knowledge_level: prediction
    agent_type: automated_agent
    publications:
    - PMID:14611657
from_schema: https://w3id.org/biolink/vocab/
aliases:
- functional association
exact_mappings:
- WBVocab:Gene-GO-Association
is_a: functional association
slot_usage:
  subject:
    name: subject
    description: gene, product or macromolecular complex that has the function associated
      with the GO term
    examples:
    - value: ZFIN:ZDB-GENE-050417-357
      description: twist1b
    range: gene
  object:
    name: object
    description: class describing the activity, process or localization of the gene
      product
    examples:
    - value: GO:0016301
      description: kinase activity
    values_from:
    - go
    range: ontology class
defining_slots:
- subject
- object