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chemical_gene_interaction_association_config.yaml
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# metamodel_version: 1.7.0# version: 3.3.2id: chemical_gene_interaction_association
schema_generating: true
description: describes a physical interaction between a chemical entity and a gene
or gene product. Any biological or chemical effect resulting from such an interaction
are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact
of a chemical on the abundance, activity, structure, etc, of either participant
in the interaction)
display_name: chemical gene interaction association
document_category: chemical gene interaction association
weight: 20
fields:
- id: id
description: A unique identifier for an entity. Must be either a CURIE shorthand
for a URI or a complete URI
display_name: id
- id: iri
description: An IRI for an entity. This is determined by the id using expansion
rules.
display_name: iri
- id: name
description: A human-readable name for an attribute or entity.
display_name: name
- id: description
description: a human-readable description of an entity
display_name: description
- id: has_attribute
description: connects any entity to an attribute
display_name: has attribute
cardinality: multi
- id: negated
description: if set to true, then the association is negated i.e. is not true
display_name: negated
- id: qualifiers
description: connects an association to qualifiers that modify or qualify the meaning
of that association
display_name: qualifiers
cardinality: multi
- id: publications
description: One or more publications that report the statement expressed in an Association,
or provide information used as evidence supporting this statement.
display_name: publications
cardinality: multi
- id: has_evidence
description: connects an association to an instance of supporting evidence
display_name: has evidence
cardinality: multi
- id: knowledge_source
description: 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.
display_name: knowledge source
- id: primary_knowledge_source
description: 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.
display_name: primary knowledge source
- id: aggregator_knowledge_source
description: 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.
display_name: aggregator knowledge source
cardinality: multi
- id: timepoint
description: a point in time
display_name: timepoint
- id: original_subject
description: 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.
display_name: original subject
- id: original_predicate
description: used to hold the original relation/predicate that an external knowledge
source uses before transformation to match the biolink-model specification.
display_name: original predicate
- id: original_object
description: 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.
display_name: original object
- id: subject_category
description: 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.
display_name: subject category
- id: object_category
description: 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.
display_name: object category
- id: subject_closure
description: 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.
display_name: subject closure
cardinality: multi
- id: object_closure
description: 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.
display_name: object closure
cardinality: multi
- id: subject_category_closure
description: 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.
display_name: subject category closure
cardinality: multi
- id: object_category_closure
description: 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.
display_name: object category closure
cardinality: multi
- id: subject_namespace
description: 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.
display_name: subject namespace
- id: object_namespace
description: 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.
display_name: object namespace
- id: subject_label_closure
description: 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.
display_name: subject label closure
cardinality: multi
- id: object_label_closure
description: 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.
display_name: object label closure
cardinality: multi
- id: retrieval_source_ids
description: 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.
display_name: retrieval source ids
cardinality: multi
- id: type
description: rdf:type of biolink:Association should be fixed at rdf:Statement
display_name: association_type
cardinality: multi
- id: category
description: "Name of the high level ontology class in which this entity is categorized.\
\ Corresponds to the label for the biolink entity type class.\n * In a neo4j database\
\ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\
\ be a biolink model class URI.\nThis 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`,\
\ ...\nIn 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}"
display_name: association_category
cardinality: multi
- id: subject_form_or_variant_qualifier
display_name: chemical gene interaction association_subject form or variant qualifier
- id: subject_part_qualifier
display_name: chemical gene interaction association_subject part qualifier
- id: subject_derivative_qualifier
display_name: chemical gene interaction association_subject derivative qualifier
- id: subject_context_qualifier
display_name: chemical gene interaction association_subject context qualifier
- id: object_form_or_variant_qualifier
display_name: chemical gene interaction association_object form or variant qualifier
- id: object_part_qualifier
display_name: chemical gene interaction association_object part qualifier
- id: object_context_qualifier
display_name: chemical gene interaction association_object context qualifier
- id: anatomical_context_qualifier
description: A statement qualifier representing an anatomical location where an
relationship expressed in an association took place (can be a tissue, cell type,
or sub-cellular location).
display_name: chemical gene interaction association_anatomical context qualifier
- id: subject
description: connects an association to the subject of the association. For example,
in a gene-to-phenotype association, the gene is subject and phenotype is object.
display_name: chemical gene interaction association_subject
- id: object
description: 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.
display_name: chemical gene interaction association_object
- id: predicate
description: A high-level grouping for the relationship type. AKA minimal predicate.
This is analogous to category for nodes.
display_name: chemical gene interaction association_predicate