Class: GeneToDiseaseOrPhenotypicFeatureAssociation
classDiagram
class GeneToDiseaseOrPhenotypicFeatureAssociation
EntityToPhenotypicFeatureAssociationMixin <|-- GeneToDiseaseOrPhenotypicFeatureAssociation
GeneToEntityAssociationMixin <|-- GeneToDiseaseOrPhenotypicFeatureAssociation
Association <|-- GeneToDiseaseOrPhenotypicFeatureAssociation
GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToPhenotypicFeatureAssociation
GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToDiseaseAssociation
GeneToDiseaseOrPhenotypicFeatureAssociation : agent_type
GeneToDiseaseOrPhenotypicFeatureAssociation --|> AgentTypeEnum : agent_type
GeneToDiseaseOrPhenotypicFeatureAssociation : aggregator_knowledge_source
GeneToDiseaseOrPhenotypicFeatureAssociation : category
GeneToDiseaseOrPhenotypicFeatureAssociation : deprecated
GeneToDiseaseOrPhenotypicFeatureAssociation : description
GeneToDiseaseOrPhenotypicFeatureAssociation : frequency_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : has_attribute
GeneToDiseaseOrPhenotypicFeatureAssociation --|> Attribute : has_attribute
GeneToDiseaseOrPhenotypicFeatureAssociation : has_count
GeneToDiseaseOrPhenotypicFeatureAssociation : has_evidence
GeneToDiseaseOrPhenotypicFeatureAssociation --|> EvidenceType : has_evidence
GeneToDiseaseOrPhenotypicFeatureAssociation : has_percentage
GeneToDiseaseOrPhenotypicFeatureAssociation : has_quotient
GeneToDiseaseOrPhenotypicFeatureAssociation : has_total
GeneToDiseaseOrPhenotypicFeatureAssociation : id
GeneToDiseaseOrPhenotypicFeatureAssociation : iri
GeneToDiseaseOrPhenotypicFeatureAssociation : knowledge_level
GeneToDiseaseOrPhenotypicFeatureAssociation --|> KnowledgeLevelEnum : knowledge_level
GeneToDiseaseOrPhenotypicFeatureAssociation : knowledge_source
GeneToDiseaseOrPhenotypicFeatureAssociation : name
GeneToDiseaseOrPhenotypicFeatureAssociation : negated
GeneToDiseaseOrPhenotypicFeatureAssociation : object
GeneToDiseaseOrPhenotypicFeatureAssociation --|> DiseaseOrPhenotypicFeature : object
GeneToDiseaseOrPhenotypicFeatureAssociation : object_aspect_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : object_category
GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : object_category
GeneToDiseaseOrPhenotypicFeatureAssociation : object_category_closure
GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : object_category_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : object_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : object_direction_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation --|> DirectionQualifierEnum : object_direction_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : object_label_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : object_namespace
GeneToDiseaseOrPhenotypicFeatureAssociation : original_object
GeneToDiseaseOrPhenotypicFeatureAssociation : original_predicate
GeneToDiseaseOrPhenotypicFeatureAssociation : original_subject
GeneToDiseaseOrPhenotypicFeatureAssociation : predicate
GeneToDiseaseOrPhenotypicFeatureAssociation : primary_knowledge_source
GeneToDiseaseOrPhenotypicFeatureAssociation : publications
GeneToDiseaseOrPhenotypicFeatureAssociation --|> Publication : publications
GeneToDiseaseOrPhenotypicFeatureAssociation : qualified_predicate
GeneToDiseaseOrPhenotypicFeatureAssociation : qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : qualifiers
GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : qualifiers
GeneToDiseaseOrPhenotypicFeatureAssociation : retrieval_source_ids
GeneToDiseaseOrPhenotypicFeatureAssociation --|> RetrievalSource : retrieval_source_ids
GeneToDiseaseOrPhenotypicFeatureAssociation : sex_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation --|> BiologicalSex : sex_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : subject
GeneToDiseaseOrPhenotypicFeatureAssociation --|> GeneOrGeneProduct : subject
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_aspect_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_category
GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : subject_category
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_category_closure
GeneToDiseaseOrPhenotypicFeatureAssociation --|> OntologyClass : subject_category_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_direction_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation --|> DirectionQualifierEnum : subject_direction_qualifier
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_label_closure
GeneToDiseaseOrPhenotypicFeatureAssociation : subject_namespace
GeneToDiseaseOrPhenotypicFeatureAssociation : timepoint
GeneToDiseaseOrPhenotypicFeatureAssociation : type
Inheritance
- Entity
- Association
- GeneToDiseaseOrPhenotypicFeatureAssociation [ EntityToPhenotypicFeatureAssociationMixin GeneToEntityAssociationMixin]
- Association
Slots
Name | Cardinality and Range | Inheritance | Examples |
---|---|---|---|
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 | |
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 | |
subject: gene in which variation is correlated with the phenotypic feature |
1..1 GeneOrGeneProduct |
Association, GeneToEntityAssociationMixin, FrequencyQualifierMixin, EntityToPhenotypicFeatureAssociationMixin | HGNC:2197 |
predicate: A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. |
1..1 PredicateType |
Association, GeneToEntityAssociationMixin, FrequencyQualifierMixin, EntityToPhenotypicFeatureAssociationMixin | |
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..1 DiseaseOrPhenotypicFeature |
Association, GeneToEntityAssociationMixin, FrequencyQualifierMixin, EntityToPhenotypicFeatureAssociationMixin | |
sex_qualifier: a qualifier used in a phenotypic association to state whether the association is specific to a particular sex. |
0..1 BiologicalSex |
EntityToPhenotypicFeatureAssociationMixin | |
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 |
0..* OntologyClass |
Association | |
publications: One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. |
0..* Publication |
Association | |
has_evidence: connects an association to an instance of supporting evidence |
0..* 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. |
0..* 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..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..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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* RetrievalSource |
Association | |
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1..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} |
0..* Uriorcurie |
Entity | |
type: rdf:type of biolink:Association should be fixed at rdf:Statement |
0..* 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 |
0..* 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 or phenotypic feature association
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 symptom/phenotype
- if the relationship of the statement using this predicate is statistical in nature,
please use `associated with likelihood` or one of its children.
from_schema: https://w3id.org/biolink/biolink-model
narrow_mappings:
- WBVocab:Gene-Phenotype-Association
- dcid:DiseaseGeneAssociation
- SIO:000983
is_a: association
mixins:
- entity to phenotypic feature association mixin
- gene to entity association mixin
slots:
- subject aspect qualifier
- object direction qualifier
slot_usage:
subject:
name: subject
description: gene in which variation is correlated with the phenotypic feature
examples:
- value: HGNC:2197
description: COL1A1 (Human)
domain_of:
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
range: gene or gene product
subject aspect qualifier:
name: subject aspect qualifier
domain_of:
- predicate mapping
- named thing associated with likelihood of named thing association
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
- gene to disease or phenotypic feature association
range: GeneOrGeneProductOrChemicalEntityAspectEnum
object:
name: object
domain_of:
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
range: disease or phenotypic feature
object direction qualifier:
name: object direction qualifier
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
- gene to disease or phenotypic feature association
- chemical entity or gene or gene product regulates gene association
range: DirectionQualifierEnum
predicate:
name: predicate
domain_of:
- predicate mapping
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
subproperty_of: affects