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Class: GeneToDiseaseAssociation

Description: An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.
classDiagram class GeneToDiseaseAssociation GeneToEntityAssociationMixin <|-- GeneToDiseaseAssociation Association <|-- GeneToDiseaseAssociation GeneToDiseaseAssociation <|-- DruggableGeneToDiseaseAssociation GeneToDiseaseAssociation <|-- GeneAsAModelOfDiseaseAssociation GeneToDiseaseAssociation <|-- GeneHasVariantThatContributesToDiseaseAssociation GeneToDiseaseAssociation : adjusted_p_value GeneToDiseaseAssociation : agent_type GeneToDiseaseAssociation --|> AgentTypeEnum : agent_type GeneToDiseaseAssociation : aggregator_knowledge_source GeneToDiseaseAssociation : allelic_requirement GeneToDiseaseAssociation : category GeneToDiseaseAssociation : deprecated GeneToDiseaseAssociation : description GeneToDiseaseAssociation : diseases_confidence_score GeneToDiseaseAssociation : elevate_to_prediction GeneToDiseaseAssociation : evidence_count GeneToDiseaseAssociation : gene2phenotype_confidence_category GeneToDiseaseAssociation : has_attribute GeneToDiseaseAssociation --|> Attribute : has_attribute GeneToDiseaseAssociation : has_confidence_score GeneToDiseaseAssociation : has_evidence GeneToDiseaseAssociation --|> InformationContentEntity : has_evidence GeneToDiseaseAssociation : has_evidence_of_type GeneToDiseaseAssociation --|> EvidenceType : has_evidence_of_type GeneToDiseaseAssociation : has_supporting_studies GeneToDiseaseAssociation --|> Study : has_supporting_studies GeneToDiseaseAssociation : id GeneToDiseaseAssociation : iri GeneToDiseaseAssociation : knowledge_level GeneToDiseaseAssociation --|> KnowledgeLevelEnum : knowledge_level GeneToDiseaseAssociation : knowledge_source GeneToDiseaseAssociation : name GeneToDiseaseAssociation : negated GeneToDiseaseAssociation : object GeneToDiseaseAssociation --|> Disease : object GeneToDiseaseAssociation : object_category GeneToDiseaseAssociation --|> OntologyClass : object_category GeneToDiseaseAssociation : object_category_closure GeneToDiseaseAssociation --|> OntologyClass : object_category_closure GeneToDiseaseAssociation : object_closure GeneToDiseaseAssociation : object_direction_qualifier GeneToDiseaseAssociation --|> DirectionQualifierEnum : object_direction_qualifier GeneToDiseaseAssociation : object_feature_name GeneToDiseaseAssociation : object_label_closure GeneToDiseaseAssociation : object_namespace GeneToDiseaseAssociation : original_object GeneToDiseaseAssociation : original_predicate GeneToDiseaseAssociation : original_subject GeneToDiseaseAssociation : p_value GeneToDiseaseAssociation : predicate GeneToDiseaseAssociation --|> GeneToDiseasePredicateEnum : predicate GeneToDiseaseAssociation : primary_knowledge_source GeneToDiseaseAssociation : publications GeneToDiseaseAssociation --|> Publication : publications GeneToDiseaseAssociation : qualified_predicate GeneToDiseaseAssociation : qualifier GeneToDiseaseAssociation : qualifiers GeneToDiseaseAssociation --|> OntologyClass : qualifiers GeneToDiseaseAssociation : retrieval_source_ids GeneToDiseaseAssociation --|> RetrievalSource : retrieval_source_ids GeneToDiseaseAssociation : semmed_agreement_count GeneToDiseaseAssociation : sources GeneToDiseaseAssociation --|> RetrievalSource : sources GeneToDiseaseAssociation : subject GeneToDiseaseAssociation --|> GeneOrGeneProduct : subject GeneToDiseaseAssociation : subject_aspect_qualifier GeneToDiseaseAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier GeneToDiseaseAssociation : subject_category GeneToDiseaseAssociation --|> OntologyClass : subject_category GeneToDiseaseAssociation : subject_category_closure GeneToDiseaseAssociation --|> OntologyClass : subject_category_closure GeneToDiseaseAssociation : subject_closure GeneToDiseaseAssociation : subject_feature_name GeneToDiseaseAssociation : subject_form_or_variant_qualifier GeneToDiseaseAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : subject_form_or_variant_qualifier GeneToDiseaseAssociation : subject_label_closure GeneToDiseaseAssociation : subject_namespace GeneToDiseaseAssociation : supporting_text GeneToDiseaseAssociation : timepoint GeneToDiseaseAssociation : type GeneToDiseaseAssociation : 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		 direct 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		 direct 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		 direct
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		 direct 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		 direct
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		 direct
subject:
gene in which variation is correlated with 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

Example values

Slot Name Value
GeneToDiseaseAssociation None
GeneToDiseaseAssociation None

LinkML Source

name: gene to disease association
description: An association between a gene or gene product and a disease, where variation
  in the gene is correlated with the disease.
comments:
- NCIT:R176 refers to the inverse relationship
- for use in describing the affect that the loss of function of a gene can have on
  exacerbating or ameliorating a disease
- if the relationship of the statement using this predicate is statistical in nature,
  please use `associated with likelihood` or one of its children.
examples:
- object:
    subject: NCBIGene:60
    predicate: biolink:associated_with
    object: MONDO:0017579
    category: biolink:GeneToDiseaseAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
- object:
    subject: UniProtKB:P11274-1
    predicate: biolink:associated_with
    object: MONDO:0011996
    category: biolink:GeneToDiseaseAssociation
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
from_schema: https://w3id.org/biolink/vocab/
exact_mappings:
- SIO:000983
close_mappings:
- dcid:DiseaseGeneAssociation
is_a: association
mixins:
- gene to entity association mixin
slots:
- subject form or variant qualifier
- subject aspect qualifier
- object direction qualifier
- allelic requirement
- qualified predicate
- diseases confidence score
- gene2phenotype confidence category
slot_usage:
  subject:
    name: subject
    description: gene in which variation is correlated with the disease
    range: gene or gene product
  subject form or variant qualifier:
    name: subject form or variant qualifier
    range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  subject aspect qualifier:
    name: subject aspect qualifier
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  object direction qualifier:
    name: object direction qualifier
    range: DirectionQualifierEnum
  object:
    name: object
    range: disease
  predicate:
    name: predicate
    range: GeneToDiseasePredicateEnum
defining_slots:
- subject
- object