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default_variant_interpretation_schema.yaml
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default_variant_interpretation_schema.yaml
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openapi: 3.0.2
servers: []
info:
version: "draft.3"
title: GA4GH Beacon Variant Interpretation Default Schema
description: >-
Schema for variant interpretations to be used as default by the Beacon.
contact:
email: [email protected]
license:
name: Apache 2.0
url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
externalDocs:
description: |
Beacon Project
url: 'http://beacon-project.io/'
paths: {}
components:
schemas:
ClinicalRelevance:
description: |
Descriptor of clinical relevance as described to the variant, including
the variant classification, the disease identifier and references of
studies supporting the association.
type: object
properties:
diseaseId:
description: |
Reference to DiseaseId from Disease object from Individual schema,
e.g. MONDO:0003582 (Hereditary breast ovarian cancer syndrome).
type: string
example: 'MONDO:0003582'
clinicalEffect: ##todo copy from variant annotation schema?
description: |
Clinical effect classification. Value from Sequence types and
features ontology (SO) variant phenotype (SO:0001769),
e.g. "disease associated variant" (SO:0001771).
type: string
enum:
- benign
- likely benign
- pathogenic
- likely pathogenic
- unknown
example: pathogenic
alleleOrigin:
description: |
Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762).
Categories are "somatic variant", "germline variant", "maternal variant",
"paternal variant", "de novo variant", "pedigree specific variant",
"population specific variant". Corresponds to Variant Inheritance in FHIR.
type: string
enum:
- 'somatic variant'
- 'germline variant'
- 'maternal variant'
- 'paternal variant'
- 'de novo variant'
- 'pedigree specific variant'
- 'population specific variant'
example: 'somatic variant'
references:
description: |
List of PUBMED ID(s) of studie(s) describing the variant-disease
association.
type: array
items:
type: string
example:
- 'PMC3623669'
- 'PMID:27153395'
phenotypicEffect:
description: |
List of annotated effect on disease.
type: object
properties:
phenotypeId:
description: |
Descriptor of phenotype found associated in this study
type: string
example: "" ##todo provide example
phenotypeEffect:
description: |
Ontology value for phenotypic effect classification determined in this study
type: string
example: '' ##todo example?
alleleOrigin:
description: |
Ontology value for allele origin of variant in sample from the Variant Origin (SO:0001762).
Categories are "somatic variant", "germline variant", "maternal variant",
"paternal variant", "de novo variant", "pedigree specific variant",
"population specific variant". Corresponds to Variant Inheritance in FHIR.
type: string
enum:
- 'somatic variant'
- 'germline variant'
- 'maternal variant'
- 'paternal variant'
- 'de novo variant'
- 'pedigree specific variant'
- 'population specific variant'
example: 'somatic variant'
references:
description: |
List of PUBMED ID(s) of studie(s) describing the variant-disease
association.
type: array
items:
type: string
example:
- 'PMC3623669'
- 'PMID:27153395'
VariantInterpretation:
description: |
Todo
type: object
properties:
variantId:
description: |
Reference to Variant ID
type: string
datasetId:
description: |
Reference to dataset ID (DatasetDetails.datasetId)
type: string
clinicalRelevance:
type: array
items:
$ref: '#/components/schemas/ClinicalRelevance'
phenotypicEffect:
type: array
items:
$ref: '#/components/schemas/phenotypicEffect'
info:
description: |
Additional unspecified metadata about the dataset response or its
content.
type: object
example:
additionalInfoKey1:
- additionalInfoValue1
- additionalInfoValue2
additionalInfoKey2: additionalInfoValue