Class: GeneToPhenotypicFeatureAssociation
URI: biolink:GeneToPhenotypicFeatureAssociation
classDiagram
class GeneToPhenotypicFeatureAssociation
EntityToPhenotypicFeatureAssociationMixin <|-- GeneToPhenotypicFeatureAssociation
GeneToEntityAssociationMixin <|-- GeneToPhenotypicFeatureAssociation
GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToPhenotypicFeatureAssociation
GeneToPhenotypicFeatureAssociation : aggregator_knowledge_source
GeneToPhenotypicFeatureAssociation : category
GeneToPhenotypicFeatureAssociation : description
GeneToPhenotypicFeatureAssociation : frequency_qualifier
GeneToPhenotypicFeatureAssociation : has_attribute
GeneToPhenotypicFeatureAssociation --|> attribute : has_attribute
GeneToPhenotypicFeatureAssociation : has_count
GeneToPhenotypicFeatureAssociation : has_evidence
GeneToPhenotypicFeatureAssociation --|> evidence type : has_evidence
GeneToPhenotypicFeatureAssociation : has_percentage
GeneToPhenotypicFeatureAssociation : has_quotient
GeneToPhenotypicFeatureAssociation : has_total
GeneToPhenotypicFeatureAssociation : id
GeneToPhenotypicFeatureAssociation : iri
GeneToPhenotypicFeatureAssociation : knowledge_source
GeneToPhenotypicFeatureAssociation : name
GeneToPhenotypicFeatureAssociation : negated
GeneToPhenotypicFeatureAssociation : object
GeneToPhenotypicFeatureAssociation --|> phenotypic feature : object
GeneToPhenotypicFeatureAssociation : object_category
GeneToPhenotypicFeatureAssociation --|> ontology class : object_category
GeneToPhenotypicFeatureAssociation : object_category_closure
GeneToPhenotypicFeatureAssociation --|> ontology class : object_category_closure
GeneToPhenotypicFeatureAssociation : object_closure
GeneToPhenotypicFeatureAssociation : object_direction_qualifier
GeneToPhenotypicFeatureAssociation --|> DirectionQualifierEnum : object_direction_qualifier
GeneToPhenotypicFeatureAssociation : object_label_closure
GeneToPhenotypicFeatureAssociation : object_namespace
GeneToPhenotypicFeatureAssociation : onset_qualifier
GeneToPhenotypicFeatureAssociation --|> onset : onset_qualifier
GeneToPhenotypicFeatureAssociation : original_object
GeneToPhenotypicFeatureAssociation : original_predicate
GeneToPhenotypicFeatureAssociation : original_subject
GeneToPhenotypicFeatureAssociation : predicate
GeneToPhenotypicFeatureAssociation : primary_knowledge_source
GeneToPhenotypicFeatureAssociation : publications
GeneToPhenotypicFeatureAssociation --|> publication : publications
GeneToPhenotypicFeatureAssociation : qualifiers
GeneToPhenotypicFeatureAssociation --|> ontology class : qualifiers
GeneToPhenotypicFeatureAssociation : retrieval_source_ids
GeneToPhenotypicFeatureAssociation --|> retrieval source : retrieval_source_ids
GeneToPhenotypicFeatureAssociation : severity_qualifier
GeneToPhenotypicFeatureAssociation --|> severity value : severity_qualifier
GeneToPhenotypicFeatureAssociation : sex_qualifier
GeneToPhenotypicFeatureAssociation --|> biological sex : sex_qualifier
GeneToPhenotypicFeatureAssociation : subject
GeneToPhenotypicFeatureAssociation --|> gene or gene product : subject
GeneToPhenotypicFeatureAssociation : subject_aspect_qualifier
GeneToPhenotypicFeatureAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier
GeneToPhenotypicFeatureAssociation : subject_category
GeneToPhenotypicFeatureAssociation --|> ontology class : subject_category
GeneToPhenotypicFeatureAssociation : subject_category_closure
GeneToPhenotypicFeatureAssociation --|> ontology class : subject_category_closure
GeneToPhenotypicFeatureAssociation : subject_closure
GeneToPhenotypicFeatureAssociation : subject_label_closure
GeneToPhenotypicFeatureAssociation : subject_namespace
GeneToPhenotypicFeatureAssociation : timepoint
GeneToPhenotypicFeatureAssociation : type
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| sex_qualifier | 0..1 BiologicalSex |
a qualifier used in a phenotypic association to state whether the association... | EntityToPhenotypicFeatureAssociationMixin |
| subject_aspect_qualifier | 0..1 GeneOrGeneProductOrChemicalEntityAspectEnum |
GeneToDiseaseOrPhenotypicFeatureAssociation | |
| object_direction_qualifier | 0..1 DirectionQualifierEnum |
GeneToDiseaseOrPhenotypicFeatureAssociation | |
| subject | 1..1 GeneOrGeneProduct |
gene in which variation is correlated with the phenotypic feature | Association |
| predicate | 1..1 PredicateType |
A high-level grouping for the relationship type | Association |
| object | 1..1 PhenotypicFeature |
connects an association to the object of the association | Association |
| negated | 0..1 Boolean |
if set to true, then the association is negated i | Association |
| qualifiers | 0..* OntologyClass |
connects an association to qualifiers that modify or qualify the meaning of t... | Association |
| publications | 0..* Publication |
One or more publications that report the statement expressed in an Associati... | Association |
| has_evidence | 0..* EvidenceType |
connects an association to an instance of supporting evidence | Association |
| knowledge_source | 0..1 String |
An Information Resource from which the knowledge expressed in an Association ... | Association |
| primary_knowledge_source | 0..1 String |
The most upstream source of the knowledge expressed in an Association that an... | Association |
| aggregator_knowledge_source | 0..* String |
An intermediate aggregator resource from which knowledge expressed in an Asso... | Association |
| timepoint | 0..1 TimeType |
a point in time | Association |
| original_subject | 0..1 String |
used to hold the original subject of a relation (or predicate) that an extern... | Association |
| original_predicate | 0..1 Uriorcurie |
used to hold the original relation/predicate that an external knowledge sourc... | Association |
| original_object | 0..1 String |
used to hold the original object of a relation (or predicate) that an externa... | Association |
| subject_category | 0..1 OntologyClass |
Used to hold the biolink class/category of an association | Association |
| object_category | 0..1 OntologyClass |
Used to hold the biolink class/category of an association | Association |
| subject_closure | 0..* String |
Used to hold the subject closure of an association | Association |
| object_closure | 0..* String |
Used to hold the object closure of an association | Association |
| subject_category_closure | 0..* OntologyClass |
Used to hold the subject category closure of an association | Association |
| object_category_closure | 0..* OntologyClass |
Used to hold the object category closure of an association | Association |
| subject_namespace | 0..1 String |
Used to hold the subject namespace of an association | Association |
| object_namespace | 0..1 String |
Used to hold the object namespace of an association | Association |
| subject_label_closure | 0..* String |
Used to hold the subject label closure of an association | Association |
| object_label_closure | 0..* String |
Used to hold the object label closure of an association | Association |
| retrieval_source_ids | 0..* RetrievalSource |
A list of retrieval sources that served as a source of knowledge expressed in... | Association |
| id | 1..1 String |
A unique identifier for an entity | Entity |
| iri | 0..1 IriType |
An IRI for an entity | Entity |
| category | 0..* CategoryType |
Name of the high level ontology class in which this entity is categorized | Entity |
| type | 0..* String |
rdf:type of biolink:Association should be fixed at rdf:Statement | Entity |
| name | 0..1 LabelType |
A human-readable name for an attribute or entity | Entity |
| description | 0..1 NarrativeText |
a human-readable description of an entity | Entity |
| has_attribute | 0..* Attribute |
connects any entity to an attribute | Entity |
| has_count | 0..1 Integer |
number of things with a particular property | FrequencyQuantifier |
| has_total | 0..1 Integer |
total number of things in a particular reference set | FrequencyQuantifier |
| has_quotient | 0..1 Double |
FrequencyQuantifier | |
| has_percentage | 0..1 Double |
equivalent to has quotient multiplied by 100 | FrequencyQuantifier |
| severity_qualifier | 0..1 SeverityValue |
a qualifier used in a phenotypic association to state how severe the phenotyp... | EntityToFeatureOrDiseaseQualifiersMixin |
| onset_qualifier | 0..1 Onset |
a qualifier used in a phenotypic association to state when the phenotype appe... | EntityToFeatureOrDiseaseQualifiersMixin |
| frequency_qualifier | 0..1 FrequencyValue |
a qualifier used in a phenotypic association to state how frequent the phenot... | FrequencyQualifierMixin |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/biolink/biolink-model
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | biolink:GeneToPhenotypicFeatureAssociation |
| native | biolink:GeneToPhenotypicFeatureAssociation |
| exact | WBVocab:Gene-Phenotype-Association |
LinkML Source
Direct
name: gene to phenotypic feature association
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- WBVocab:Gene-Phenotype-Association
is_a: gene to disease or phenotypic feature association
mixins:
- entity to phenotypic feature association mixin
- gene to entity association mixin
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
range: gene or gene product
object:
name: object
domain_of:
- association
range: phenotypic feature
defining_slots:
- subject
- object