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Class: GeneHasVariantThatContributesToDiseaseAssociation

Description: A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution.
classDiagram class GeneHasVariantThatContributesToDiseaseAssociation GeneToDiseaseAssociation <|-- GeneHasVariantThatContributesToDiseaseAssociation GeneHasVariantThatContributesToDiseaseAssociation : adjusted_p_value GeneHasVariantThatContributesToDiseaseAssociation : agent_type GeneHasVariantThatContributesToDiseaseAssociation --|> AgentTypeEnum : agent_type GeneHasVariantThatContributesToDiseaseAssociation : aggregator_knowledge_source GeneHasVariantThatContributesToDiseaseAssociation : allelic_requirement GeneHasVariantThatContributesToDiseaseAssociation : category GeneHasVariantThatContributesToDiseaseAssociation : deprecated GeneHasVariantThatContributesToDiseaseAssociation : description GeneHasVariantThatContributesToDiseaseAssociation : diseases_confidence_score GeneHasVariantThatContributesToDiseaseAssociation : elevate_to_prediction GeneHasVariantThatContributesToDiseaseAssociation : evidence_count GeneHasVariantThatContributesToDiseaseAssociation : gene2phenotype_confidence_category GeneHasVariantThatContributesToDiseaseAssociation : has_attribute GeneHasVariantThatContributesToDiseaseAssociation --|> Attribute : has_attribute GeneHasVariantThatContributesToDiseaseAssociation : has_confidence_score GeneHasVariantThatContributesToDiseaseAssociation : has_evidence GeneHasVariantThatContributesToDiseaseAssociation --|> InformationContentEntity : has_evidence GeneHasVariantThatContributesToDiseaseAssociation : has_evidence_of_type GeneHasVariantThatContributesToDiseaseAssociation --|> EvidenceType : has_evidence_of_type GeneHasVariantThatContributesToDiseaseAssociation : has_supporting_studies GeneHasVariantThatContributesToDiseaseAssociation --|> Study : has_supporting_studies GeneHasVariantThatContributesToDiseaseAssociation : id GeneHasVariantThatContributesToDiseaseAssociation : iri GeneHasVariantThatContributesToDiseaseAssociation : knowledge_level GeneHasVariantThatContributesToDiseaseAssociation --|> KnowledgeLevelEnum : knowledge_level GeneHasVariantThatContributesToDiseaseAssociation : knowledge_source GeneHasVariantThatContributesToDiseaseAssociation : name GeneHasVariantThatContributesToDiseaseAssociation : negated GeneHasVariantThatContributesToDiseaseAssociation : object GeneHasVariantThatContributesToDiseaseAssociation --|> Disease : object GeneHasVariantThatContributesToDiseaseAssociation : object_category GeneHasVariantThatContributesToDiseaseAssociation --|> OntologyClass : object_category GeneHasVariantThatContributesToDiseaseAssociation : object_category_closure GeneHasVariantThatContributesToDiseaseAssociation --|> OntologyClass : object_category_closure GeneHasVariantThatContributesToDiseaseAssociation : object_closure GeneHasVariantThatContributesToDiseaseAssociation : object_direction_qualifier GeneHasVariantThatContributesToDiseaseAssociation --|> DirectionQualifierEnum : object_direction_qualifier GeneHasVariantThatContributesToDiseaseAssociation : object_feature_name GeneHasVariantThatContributesToDiseaseAssociation : object_label_closure GeneHasVariantThatContributesToDiseaseAssociation : object_namespace GeneHasVariantThatContributesToDiseaseAssociation : original_object GeneHasVariantThatContributesToDiseaseAssociation : original_predicate GeneHasVariantThatContributesToDiseaseAssociation : original_subject GeneHasVariantThatContributesToDiseaseAssociation : p_value GeneHasVariantThatContributesToDiseaseAssociation : predicate GeneHasVariantThatContributesToDiseaseAssociation --|> GeneToDiseasePredicateEnum : predicate GeneHasVariantThatContributesToDiseaseAssociation : primary_knowledge_source GeneHasVariantThatContributesToDiseaseAssociation : publications GeneHasVariantThatContributesToDiseaseAssociation --|> Publication : publications GeneHasVariantThatContributesToDiseaseAssociation : qualified_predicate GeneHasVariantThatContributesToDiseaseAssociation : qualifier GeneHasVariantThatContributesToDiseaseAssociation : qualifiers GeneHasVariantThatContributesToDiseaseAssociation --|> OntologyClass : qualifiers GeneHasVariantThatContributesToDiseaseAssociation : retrieval_source_ids GeneHasVariantThatContributesToDiseaseAssociation --|> RetrievalSource : retrieval_source_ids GeneHasVariantThatContributesToDiseaseAssociation : semmed_agreement_count GeneHasVariantThatContributesToDiseaseAssociation : sources GeneHasVariantThatContributesToDiseaseAssociation --|> RetrievalSource : sources GeneHasVariantThatContributesToDiseaseAssociation : subject GeneHasVariantThatContributesToDiseaseAssociation --|> GeneOrGeneProduct : subject GeneHasVariantThatContributesToDiseaseAssociation : subject_aspect_qualifier GeneHasVariantThatContributesToDiseaseAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier GeneHasVariantThatContributesToDiseaseAssociation : subject_category GeneHasVariantThatContributesToDiseaseAssociation --|> OntologyClass : subject_category GeneHasVariantThatContributesToDiseaseAssociation : subject_category_closure GeneHasVariantThatContributesToDiseaseAssociation --|> OntologyClass : subject_category_closure GeneHasVariantThatContributesToDiseaseAssociation : subject_closure GeneHasVariantThatContributesToDiseaseAssociation : subject_feature_name GeneHasVariantThatContributesToDiseaseAssociation : subject_form_or_variant_qualifier GeneHasVariantThatContributesToDiseaseAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : subject_form_or_variant_qualifier GeneHasVariantThatContributesToDiseaseAssociation : subject_label_closure GeneHasVariantThatContributesToDiseaseAssociation : subject_namespace GeneHasVariantThatContributesToDiseaseAssociation : supporting_text GeneHasVariantThatContributesToDiseaseAssociation : timepoint GeneHasVariantThatContributesToDiseaseAssociation : type GeneHasVariantThatContributesToDiseaseAssociation : update_date

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject_form_or_variant_qualifier:
A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement).
0..1
ChemicalOrGeneOrGeneProductFormOrVariantEnum		 direct mutation, late stage, severe, transplant, chemical analog
subject_aspect_qualifier:
Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement). 		0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 GeneToDiseaseAssociation stability, abundance, expression, exposure
object_direction_qualifier:
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). 		0..1
DirectionQualifierEnum		 GeneToDiseaseAssociation increased, downregulated
allelic_requirement:
The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance. 		0..1
String		 GeneToDiseaseAssociation
qualified_predicate:
Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. 		0..1
Uriorcurie		 GeneToDiseaseAssociation biolink:causes
diseases_confidence_score:
A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations, but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale. 		0..1
Float		 GeneToDiseaseAssociation
gene2phenotype_confidence_category:
A term used by EBI Gene2Phenotype to describe the confidence that the association is real. GenCC confidence terms are used for different levels of confidence (enum). See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section. 		0..1
String		 GeneToDiseaseAssociation
subject:
A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease. 		1
GeneOrGeneProduct		 GeneToEntityAssociationMixin, Association
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
GeneToDiseasePredicateEnum		 GeneToEntityAssociationMixin, Association
object:
connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. 		1
Disease		 GeneToEntityAssociationMixin, Association
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

LinkML Source

name: gene has variant that contributes to disease association
description: A gene-to-disease association that is asserted on the grounds that the
  gene harbours a sequence variant that contributes to the disease. Qualifies the
  gene with the form or variant that underlies the contribution.
from_schema: https://w3id.org/biolink/vocab/
is_a: gene to disease association
slots:
- subject form or variant qualifier
slot_usage:
  subject:
    name: subject
    description: A gene that has a role in modeling the disease. This may be a model
      organism ortholog of a known disease gene, or it may be a gene whose mutants
      recapitulate core features of the disease.
    range: gene or gene product
  object:
    name: object
    range: disease
  predicate:
    name: predicate
    subproperty_of: contributes to
defining_slots:
- subject
- predicate
- object