Skip to content

Commit

Permalink
add changes to reflect #1216
Browse files Browse the repository at this point in the history
  • Loading branch information
sierra-moxon committed Apr 26, 2023
1 parent 8d6d2eb commit 98b700d
Showing 1 changed file with 47 additions and 37 deletions.
84 changes: 47 additions & 37 deletions biolink-model.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3094,18 +3094,28 @@ slots:
# Despite the name, note that this particular entity is
# NOT a biolink:Association but rather, a biolink:predicate
genetic association:
is_a: related to at instance level
deprecated: true
deprecated_element_has_exact_replacement: genetically associated with
is_a: associated with
symmetric: true
annotations:
canonical_predicate: true

genetically associated with:
is_a: associated with
description: >-
Co-occurrence of a certain allele of a genetic marker and the phenotype
of interest in the same individuals at above-chance level
exact_mappings:
- WIKIDATA_PROPERTY:P2293
symmetric: true
annotations:
canonical_predicate: true
description: >-
Co-occurrence of a certain allele of a genetic marker and the phenotype
of interest in the same individuals at above-chance level
exact_mappings:
- WIKIDATA_PROPERTY:P2293
in_subset:
- translator_minimal


gene associated with condition:
is_a: genetic association
is_a: genetically associated with
description: >-
holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence,
contribute to, or correlate with
Expand All @@ -3125,7 +3135,7 @@ slots:
- NCIT:R48

condition associated with gene:
is_a: genetic association
is_a: genetically associated with
aliases: ['disease associated with gene']
description: >-
holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
Expand Down Expand Up @@ -9703,48 +9713,48 @@ classes:
- value: ClinGen:CA024716
description: "chr13:g.32921033G>C (hg19) in ClinGen"

gene to phenotypic feature association:
gene to disease or phenotypic feature association:
is_a: association
exact_mappings:
- WBVocab:Gene-Phenotype-Association
defining_slots:
- subject
- object
mixins:
- entity to phenotypic feature association mixin
- gene to entity association mixin
narrow_mappings:
- WBVocab:Gene-Phenotype-Association
- dcid:DiseaseGeneAssociation
- SIO:000983
slots:
- subject aspect qualifier
- object direction qualifier
slot_usage:
subject:
range: gene or gene product
description: "gene in which variation is correlated with the phenotypic feature"
examples:
- value: HGNC:2197
description: "COL1A1 (Human)"
subject aspect qualifier:
range: GeneOrGeneProductOrChemicalEntityAspectEnum
object:
range: phenotypic feature
range: disease or phenotypic feature
object direction qualifier:
range: DirectionQualifierEnum
predicate:
range:
subproperty_of: affects
comments:
- NCIT:R176 refers to the inverse relationship
- for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype
- if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.

gene to disease association:
deprecated: true
deprecated_element_has_exact_replacement: gene to disease or phenotypic feature association
is_a: association

gene to phenotype association:
deprecated: true
deprecated_element_has_exact_replacement: gene to disease or phenotypic feature association
is_a: association
comments:
- NCIT:R176 refers to the inverse relationship
exact_mappings:
- SIO:000983
close_mappings:
- dcid:DiseaseGeneAssociation
defining_slots:
- subject
- object
mixins:
- entity to disease association mixin
- gene to entity association mixin
slot_usage:
subject:
range: gene or gene product
description: >-
gene in which variation is correlated with the disease,
may be protective or causative or associative, or as a model
object:
range: disease

druggable gene to disease association:
is_a: gene to disease association
Expand Down Expand Up @@ -9782,7 +9792,7 @@ classes:
object:
range: gene
predicate:
subproperty_of: genetic association
subproperty_of: genetically associated with

variant to gene expression association:
description: >-
Expand Down

0 comments on commit 98b700d

Please sign in to comment.