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Class: GeneToPhenotypicFeatureAssociation

classDiagram class GeneToPhenotypicFeatureAssociation EntityToPhenotypicFeatureAssociationMixin <|-- GeneToPhenotypicFeatureAssociation GeneToEntityAssociationMixin <|-- GeneToPhenotypicFeatureAssociation GeneToDiseaseOrPhenotypicFeatureAssociation <|-- GeneToPhenotypicFeatureAssociation GeneToPhenotypicFeatureAssociation : agent_type GeneToPhenotypicFeatureAssociation --|> AgentTypeEnum : agent_type GeneToPhenotypicFeatureAssociation : aggregator_knowledge_source GeneToPhenotypicFeatureAssociation : category GeneToPhenotypicFeatureAssociation : deprecated GeneToPhenotypicFeatureAssociation : description GeneToPhenotypicFeatureAssociation : frequency_qualifier GeneToPhenotypicFeatureAssociation : has_attribute GeneToPhenotypicFeatureAssociation --|> Attribute : has_attribute GeneToPhenotypicFeatureAssociation : has_count GeneToPhenotypicFeatureAssociation : has_evidence GeneToPhenotypicFeatureAssociation --|> EvidenceType : has_evidence GeneToPhenotypicFeatureAssociation : has_percentage GeneToPhenotypicFeatureAssociation : has_quotient GeneToPhenotypicFeatureAssociation : has_total GeneToPhenotypicFeatureAssociation : id GeneToPhenotypicFeatureAssociation : iri GeneToPhenotypicFeatureAssociation : knowledge_level GeneToPhenotypicFeatureAssociation --|> KnowledgeLevelEnum : knowledge_level GeneToPhenotypicFeatureAssociation : knowledge_source GeneToPhenotypicFeatureAssociation : name GeneToPhenotypicFeatureAssociation : negated GeneToPhenotypicFeatureAssociation : object GeneToPhenotypicFeatureAssociation --|> PhenotypicFeature : object GeneToPhenotypicFeatureAssociation : object_aspect_qualifier GeneToPhenotypicFeatureAssociation : object_category GeneToPhenotypicFeatureAssociation --|> OntologyClass : object_category GeneToPhenotypicFeatureAssociation : object_category_closure GeneToPhenotypicFeatureAssociation --|> OntologyClass : object_category_closure GeneToPhenotypicFeatureAssociation : object_closure GeneToPhenotypicFeatureAssociation : object_direction_qualifier GeneToPhenotypicFeatureAssociation --|> DirectionQualifierEnum : object_direction_qualifier GeneToPhenotypicFeatureAssociation : object_label_closure GeneToPhenotypicFeatureAssociation : object_namespace GeneToPhenotypicFeatureAssociation : original_object GeneToPhenotypicFeatureAssociation : original_predicate GeneToPhenotypicFeatureAssociation : original_subject GeneToPhenotypicFeatureAssociation : predicate GeneToPhenotypicFeatureAssociation : primary_knowledge_source GeneToPhenotypicFeatureAssociation : publications GeneToPhenotypicFeatureAssociation --|> Publication : publications GeneToPhenotypicFeatureAssociation : qualified_predicate GeneToPhenotypicFeatureAssociation : qualifier GeneToPhenotypicFeatureAssociation : qualifiers GeneToPhenotypicFeatureAssociation --|> OntologyClass : qualifiers GeneToPhenotypicFeatureAssociation : retrieval_source_ids GeneToPhenotypicFeatureAssociation --|> RetrievalSource : retrieval_source_ids GeneToPhenotypicFeatureAssociation : sex_qualifier GeneToPhenotypicFeatureAssociation --|> BiologicalSex : sex_qualifier GeneToPhenotypicFeatureAssociation : subject GeneToPhenotypicFeatureAssociation --|> GeneOrGeneProduct : subject GeneToPhenotypicFeatureAssociation : subject_aspect_qualifier GeneToPhenotypicFeatureAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier GeneToPhenotypicFeatureAssociation : subject_category GeneToPhenotypicFeatureAssociation --|> OntologyClass : subject_category GeneToPhenotypicFeatureAssociation : subject_category_closure GeneToPhenotypicFeatureAssociation --|> OntologyClass : subject_category_closure GeneToPhenotypicFeatureAssociation : subject_closure GeneToPhenotypicFeatureAssociation : subject_direction_qualifier GeneToPhenotypicFeatureAssociation --|> DirectionQualifierEnum : subject_direction_qualifier GeneToPhenotypicFeatureAssociation : subject_label_closure GeneToPhenotypicFeatureAssociation : subject_namespace GeneToPhenotypicFeatureAssociation : timepoint GeneToPhenotypicFeatureAssociation : type

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
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
PhenotypicFeature
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
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
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
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 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
    - 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
  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: phenotypic feature
defining_slots:
- subject
- object