Class: CellLineAsAModelOfDiseaseAssociation
classDiagram
class CellLineAsAModelOfDiseaseAssociation
ModelToDiseaseAssociationMixin <|-- CellLineAsAModelOfDiseaseAssociation
EntityToDiseaseAssociationMixin <|-- CellLineAsAModelOfDiseaseAssociation
CellLineToDiseaseOrPhenotypicFeatureAssociation <|-- CellLineAsAModelOfDiseaseAssociation
CellLineAsAModelOfDiseaseAssociation : agent_type
CellLineAsAModelOfDiseaseAssociation --|> AgentTypeEnum : agent_type
CellLineAsAModelOfDiseaseAssociation : aggregator_knowledge_source
CellLineAsAModelOfDiseaseAssociation : category
CellLineAsAModelOfDiseaseAssociation : deprecated
CellLineAsAModelOfDiseaseAssociation : description
CellLineAsAModelOfDiseaseAssociation : frequency_qualifier
CellLineAsAModelOfDiseaseAssociation : has_attribute
CellLineAsAModelOfDiseaseAssociation --|> Attribute : has_attribute
CellLineAsAModelOfDiseaseAssociation : has_evidence
CellLineAsAModelOfDiseaseAssociation --|> EvidenceType : has_evidence
CellLineAsAModelOfDiseaseAssociation : id
CellLineAsAModelOfDiseaseAssociation : iri
CellLineAsAModelOfDiseaseAssociation : knowledge_level
CellLineAsAModelOfDiseaseAssociation --|> KnowledgeLevelEnum : knowledge_level
CellLineAsAModelOfDiseaseAssociation : knowledge_source
CellLineAsAModelOfDiseaseAssociation : name
CellLineAsAModelOfDiseaseAssociation : negated
CellLineAsAModelOfDiseaseAssociation : object
CellLineAsAModelOfDiseaseAssociation --|> Disease : object
CellLineAsAModelOfDiseaseAssociation : object_aspect_qualifier
CellLineAsAModelOfDiseaseAssociation : object_category
CellLineAsAModelOfDiseaseAssociation --|> OntologyClass : object_category
CellLineAsAModelOfDiseaseAssociation : object_category_closure
CellLineAsAModelOfDiseaseAssociation --|> OntologyClass : object_category_closure
CellLineAsAModelOfDiseaseAssociation : object_closure
CellLineAsAModelOfDiseaseAssociation : object_direction_qualifier
CellLineAsAModelOfDiseaseAssociation --|> DirectionQualifierEnum : object_direction_qualifier
CellLineAsAModelOfDiseaseAssociation : object_label_closure
CellLineAsAModelOfDiseaseAssociation : object_namespace
CellLineAsAModelOfDiseaseAssociation : original_object
CellLineAsAModelOfDiseaseAssociation : original_predicate
CellLineAsAModelOfDiseaseAssociation : original_subject
CellLineAsAModelOfDiseaseAssociation : predicate
CellLineAsAModelOfDiseaseAssociation : primary_knowledge_source
CellLineAsAModelOfDiseaseAssociation : publications
CellLineAsAModelOfDiseaseAssociation --|> Publication : publications
CellLineAsAModelOfDiseaseAssociation : qualified_predicate
CellLineAsAModelOfDiseaseAssociation : qualifier
CellLineAsAModelOfDiseaseAssociation : qualifiers
CellLineAsAModelOfDiseaseAssociation --|> OntologyClass : qualifiers
CellLineAsAModelOfDiseaseAssociation : retrieval_source_ids
CellLineAsAModelOfDiseaseAssociation --|> RetrievalSource : retrieval_source_ids
CellLineAsAModelOfDiseaseAssociation : subject
CellLineAsAModelOfDiseaseAssociation --|> CellLine : subject
CellLineAsAModelOfDiseaseAssociation : subject_aspect_qualifier
CellLineAsAModelOfDiseaseAssociation : subject_category
CellLineAsAModelOfDiseaseAssociation --|> OntologyClass : subject_category
CellLineAsAModelOfDiseaseAssociation : subject_category_closure
CellLineAsAModelOfDiseaseAssociation --|> OntologyClass : subject_category_closure
CellLineAsAModelOfDiseaseAssociation : subject_closure
CellLineAsAModelOfDiseaseAssociation : subject_direction_qualifier
CellLineAsAModelOfDiseaseAssociation --|> DirectionQualifierEnum : subject_direction_qualifier
CellLineAsAModelOfDiseaseAssociation : subject_label_closure
CellLineAsAModelOfDiseaseAssociation : subject_namespace
CellLineAsAModelOfDiseaseAssociation : timepoint
CellLineAsAModelOfDiseaseAssociation : type
Inheritance
Slots
Name | Cardinality and Range | Inheritance | Examples |
---|---|---|---|
subject: A cell line derived from an organismal entity with a disease state that is used as a model of that disease. |
1..1 CellLine |
CellLineToEntityAssociationMixin, ModelToDiseaseAssociationMixin, Association, FrequencyQualifierMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin | |
predicate: The relationship to the disease |
1..1 PredicateType |
CellLineToEntityAssociationMixin, ModelToDiseaseAssociationMixin, Association, FrequencyQualifierMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin | |
object: disease |
1..1 Disease |
CellLineToEntityAssociationMixin, ModelToDiseaseAssociationMixin, Association, FrequencyQualifierMixin, EntityToDiseaseOrPhenotypicFeatureAssociationMixin | MONDO:0020066 |
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 | |
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 String |
EntityToFeatureOrDiseaseQualifiersMixin | stability, abundance, expression, exposure |
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 |
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 |
EntityToFeatureOrDiseaseQualifiersMixin | |
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: cell line as a model of disease association
from_schema: https://w3id.org/biolink/biolink-model
is_a: cell line to disease or phenotypic feature association
mixins:
- model to disease association mixin
- entity to disease association mixin
slot_usage:
subject:
name: subject
description: A cell line derived from an organismal entity with a disease state
that is used as a model of that disease.
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: cell line
defining_slots:
- subject
- predicate
- object