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Class: VariantToPopulationAssociation

Description: An association between a variant and a population, where the variant has particular frequency in the population
classDiagram class VariantToPopulationAssociation VariantToEntityAssociationMixin <|-- VariantToPopulationAssociation FrequencyQuantifier <|-- VariantToPopulationAssociation FrequencyQualifierMixin <|-- VariantToPopulationAssociation Association <|-- VariantToPopulationAssociation VariantToPopulationAssociation : agent_type VariantToPopulationAssociation --|> AgentTypeEnum : agent_type VariantToPopulationAssociation : aggregator_knowledge_source VariantToPopulationAssociation : category VariantToPopulationAssociation : deprecated VariantToPopulationAssociation : description VariantToPopulationAssociation : frequency_qualifier VariantToPopulationAssociation : has_attribute VariantToPopulationAssociation --|> Attribute : has_attribute VariantToPopulationAssociation : has_count VariantToPopulationAssociation : has_evidence VariantToPopulationAssociation --|> EvidenceType : has_evidence VariantToPopulationAssociation : has_percentage VariantToPopulationAssociation : has_quotient VariantToPopulationAssociation : has_total VariantToPopulationAssociation : id VariantToPopulationAssociation : iri VariantToPopulationAssociation : knowledge_level VariantToPopulationAssociation --|> KnowledgeLevelEnum : knowledge_level VariantToPopulationAssociation : knowledge_source VariantToPopulationAssociation : name VariantToPopulationAssociation : negated VariantToPopulationAssociation : object VariantToPopulationAssociation --|> PopulationOfIndividualOrganisms : object VariantToPopulationAssociation : object_category VariantToPopulationAssociation --|> OntologyClass : object_category VariantToPopulationAssociation : object_category_closure VariantToPopulationAssociation --|> OntologyClass : object_category_closure VariantToPopulationAssociation : object_closure VariantToPopulationAssociation : object_label_closure VariantToPopulationAssociation : object_namespace VariantToPopulationAssociation : original_object VariantToPopulationAssociation : original_predicate VariantToPopulationAssociation : original_subject VariantToPopulationAssociation : predicate VariantToPopulationAssociation : primary_knowledge_source VariantToPopulationAssociation : publications VariantToPopulationAssociation --|> Publication : publications VariantToPopulationAssociation : qualifier VariantToPopulationAssociation : qualifiers VariantToPopulationAssociation --|> OntologyClass : qualifiers VariantToPopulationAssociation : retrieval_source_ids VariantToPopulationAssociation --|> RetrievalSource : retrieval_source_ids VariantToPopulationAssociation : subject VariantToPopulationAssociation --|> SequenceVariant : subject VariantToPopulationAssociation : subject_category VariantToPopulationAssociation --|> OntologyClass : subject_category VariantToPopulationAssociation : subject_category_closure VariantToPopulationAssociation --|> OntologyClass : subject_category_closure VariantToPopulationAssociation : subject_closure VariantToPopulationAssociation : subject_label_closure VariantToPopulationAssociation : subject_namespace VariantToPopulationAssociation : timepoint VariantToPopulationAssociation : type

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
subject:
an allele that has a certain frequency in a given population
1..1
SequenceVariant		 Association, VariantToEntityAssociationMixin, FrequencyQualifierMixin NC_000017.11:g.43051071A>T
predicate:
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. 		1..1
PredicateType		 Association, VariantToEntityAssociationMixin, FrequencyQualifierMixin
object:
the population that is observed to have the frequency 		1..1
PopulationOfIndividualOrganisms		 Association, VariantToEntityAssociationMixin, FrequencyQualifierMixin HANCESTRO:0010
has_count:
number in object population that carry a particular allele, aka allele count 		0..1
Integer		 FrequencyQuantifier 4
has_total:
number all populations that carry a particular allele, aka allele number 		0..1
Integer		 FrequencyQuantifier 24014
has_quotient:
frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency 		0..1
Double		 FrequencyQuantifier 0.0001666
has_percentage:
equivalent to has quotient multiplied by 100 		0..1
Double		 FrequencyQuantifier
frequency_qualifier:
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject 		0..1
FrequencyValue		 FrequencyQualifierMixin
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

LinkML Source

name: variant to population association
description: An association between a variant and a population, where the variant
  has particular frequency in the population
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
mixins:
- variant to entity association mixin
- frequency quantifier
- frequency qualifier mixin
slot_usage:
  subject:
    name: subject
    description: an allele that has a certain frequency in a given population
    examples:
    - value: NC_000017.11:g.43051071A>T
      description: 17:41203088 A/C in gnomad
    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: sequence variant
  object:
    name: object
    description: the population that is observed to have the frequency
    examples:
    - value: HANCESTRO:0010
      description: African
    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: population of individual organisms
  has quotient:
    name: has quotient
    description: frequency of allele in population, expressed as a number with allele
      divided by number in reference population, aka allele frequency
    examples:
    - value: '0.0001666'
    domain_of:
    - frequency quantifier
  has count:
    name: has count
    description: number in object population that carry a particular allele, aka allele
      count
    examples:
    - value: '4'
      description: 4 individuals in gnomad set
    domain_of:
    - frequency quantifier
  has total:
    name: has total
    description: number all populations that carry a particular allele, aka allele
      number
    examples:
    - value: '24014'
      description: 24014 individuals in gnomad set
    domain_of:
    - frequency quantifier
defining_slots:
- subject
- object