Class: GeneToDiseaseAssociation
classDiagram
class GeneToDiseaseAssociation
EntityToDiseaseAssociationMixin <|-- GeneToDiseaseAssociation
GeneToEntityAssociationMixin <|-- GeneToDiseaseAssociation
GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToDiseaseAssociation
GeneToDiseaseAssociation <|-- CausalGeneToDiseaseAssociation
GeneToDiseaseAssociation <|-- CorrelatedGeneToDiseaseAssociation
GeneToDiseaseAssociation <|-- DruggableGeneToDiseaseAssociation
GeneToDiseaseAssociation <|-- GeneAsAModelOfDiseaseAssociation
GeneToDiseaseAssociation <|-- GeneHasVariantThatContributesToDiseaseAssociation
GeneToDiseaseAssociation : adjusted_p_value
GeneToDiseaseAssociation : agent_type
GeneToDiseaseAssociation --|> AgentTypeEnum : agent_type
GeneToDiseaseAssociation : aggregator_knowledge_source
GeneToDiseaseAssociation : anatomical_context_qualifier
GeneToDiseaseAssociation : category
GeneToDiseaseAssociation : deprecated
GeneToDiseaseAssociation : description
GeneToDiseaseAssociation : disease_context_qualifier
GeneToDiseaseAssociation --|> Disease : disease_context_qualifier
GeneToDiseaseAssociation : frequency_qualifier
GeneToDiseaseAssociation : has_attribute
GeneToDiseaseAssociation --|> Attribute : has_attribute
GeneToDiseaseAssociation : has_count
GeneToDiseaseAssociation : has_evidence
GeneToDiseaseAssociation --|> EvidenceType : has_evidence
GeneToDiseaseAssociation : has_percentage
GeneToDiseaseAssociation : has_quotient
GeneToDiseaseAssociation : has_supporting_studies
GeneToDiseaseAssociation --|> Study : has_supporting_studies
GeneToDiseaseAssociation : has_total
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_aspect_qualifier
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_label_closure
GeneToDiseaseAssociation : object_namespace
GeneToDiseaseAssociation : object_specialization_qualifier
GeneToDiseaseAssociation : original_object
GeneToDiseaseAssociation : original_predicate
GeneToDiseaseAssociation : original_subject
GeneToDiseaseAssociation : p_value
GeneToDiseaseAssociation : 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 : sex_qualifier
GeneToDiseaseAssociation --|> BiologicalSex : sex_qualifier
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_direction_qualifier
GeneToDiseaseAssociation --|> DirectionQualifierEnum : subject_direction_qualifier
GeneToDiseaseAssociation : subject_label_closure
GeneToDiseaseAssociation : subject_namespace
GeneToDiseaseAssociation : subject_specialization_qualifier
GeneToDiseaseAssociation : timepoint
GeneToDiseaseAssociation : type
Inheritance
- Entity
- Association
- GeneToDiseaseOrPhenotypicFeatureAssociation [ EntityToPhenotypicFeatureAssociationMixin GeneToEntityAssociationMixin]
- GeneToDiseaseAssociation [ EntityToDiseaseAssociationMixin GeneToEntityAssociationMixin]
- CausalGeneToDiseaseAssociation [ EntityToDiseaseAssociationMixin GeneToEntityAssociationMixin]
- CorrelatedGeneToDiseaseAssociation [ EntityToDiseaseAssociationMixin GeneToEntityAssociationMixin]
- DruggableGeneToDiseaseAssociation [ EntityToDiseaseAssociationMixin GeneToEntityAssociationMixin]
- GeneAsAModelOfDiseaseAssociation [ ModelToDiseaseAssociationMixin EntityToDiseaseAssociationMixin]
- GeneHasVariantThatContributesToDiseaseAssociation
- GeneToDiseaseAssociation [ EntityToDiseaseAssociationMixin GeneToEntityAssociationMixin]
- GeneToDiseaseOrPhenotypicFeatureAssociation [ EntityToPhenotypicFeatureAssociationMixin GeneToEntityAssociationMixin]
- Association
Slots
Name | Cardinality and Range | Inheritance | Examples |
---|---|---|---|
subject: gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model |
1 GeneOrGeneProduct |
GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association | HGNC:2197 |
predicate: A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. |
1 PredicateType |
GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association | |
object: disease |
1 Disease |
GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, FrequencyQualifierMixin, Association | MONDO:0020066 |
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 |
GeneToDiseaseOrPhenotypicFeatureAssociation, EntityToFeatureOrDiseaseQualifiersMixin | 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 |
GeneToDiseaseOrPhenotypicFeatureAssociation, EntityToFeatureOrDiseaseQualifiersMixin | |
sex_qualifier: a qualifier used in a phenotypic association to state whether the association is specific to a particular sex. |
0..1 BiologicalSex |
EntityToPhenotypicFeatureAssociationMixin | |
disease_context_qualifier: A context qualifier representing a disease or condition in which a relationship expressed in an association took place. |
0..1 Disease |
EntityToPhenotypicFeatureAssociationMixin, EntityToFeatureOrDiseaseQualifiersMixin | MONDO:0004979, MONDO:0005148 |
subject_specialization_qualifier: A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. |
0..1 Uriorcurie |
EntityToPhenotypicFeatureAssociationMixin | |
object_specialization_qualifier: A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier. |
0..1 Uriorcurie |
EntityToPhenotypicFeatureAssociationMixin | |
anatomical_context_qualifier: A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location). |
0..1 String |
EntityToPhenotypicFeatureAssociationMixin | blood, cerebral cortext |
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 | |
has_evidence: connects an association to an instance of supporting evidence |
* EvidenceType |
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_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 | ['BRACA1'] |
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 | |
has_supporting_studies: A study that produced information used as evidence to generate the knowledge expressed in an Association. |
* Study |
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 | |
has_count: number of things with a particular property |
0..1 Integer |
FrequencyQuantifier | |
has_total: total number of things in a particular reference set |
0..1 Integer |
FrequencyQuantifier | |
has_quotient: None |
0..1 Double |
FrequencyQuantifier | |
has_percentage: equivalent to has quotient multiplied by 100 |
0..1 Double |
FrequencyQuantifier | |
subject_direction_qualifier: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). |
0..1 DirectionQualifierEnum |
EntityToFeatureOrDiseaseQualifiersMixin | |
object_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 object of an association (aka: statement). |
0..1 String |
EntityToFeatureOrDiseaseQualifiersMixin | stability, abundance, expression, exposure |
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. 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 String |
EntityToFeatureOrDiseaseQualifiersMixin | |
frequency_qualifier: a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject |
0..1 FrequencyValue |
FrequencyQualifierMixin |
LinkML Source
name: gene to disease association
comments:
- NCIT:R176 refers to the inverse relationship
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- SIO:000983
close_mappings:
- dcid:DiseaseGeneAssociation
is_a: gene to disease or phenotypic feature association
mixins:
- entity to disease association mixin
- gene to entity association mixin
slot_usage:
subject:
name: subject
description: gene in which variation is correlated with the disease, may be protective
or causative or associative, or as a model
range: gene or gene product
object:
name: object
range: disease
defining_slots:
- subject
- object