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Family.yaml
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Family.yaml
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"$schema": http://json-schema.org/draft-07/schema#
"$id": https://schemablocks.org/schemas/sb-phenopackets/Family/v1.0.0
title: Family
description: |
Phenotype, sample and pedigree data required for a genomic diagnosis.
Equivalent to the Genomics England InterpretationRequestRD
https://github.com/genomicsengland/GelReportModels/blob/master/schemas/IDLs/org.gel.models.report.avro/5.0.0/InterpretationRequestRD.avdl
type: object
meta:
contributors:
- description: "GA4GH Data Working Group"
- description: "Jules Jacobsen"
id: "orcid:0000-0002-3265-15918"
- description: "Peter Robinson"
id: "orcid:0000-0002-0736-91998"
- description: "Michael Baudis"
id: "orcid:0000-0002-9903-4248"
- description: "Melanie Courtot"
id: "orcid:0000-0002-9551-6370"
- description: "Isuru Liyanage"
id: "orcid:0000-0002-4839-5158"
provenance:
- description: Phenopackets
id: 'https://github.com/phenopackets/phenopacket-schema/blob/master/docs/family.rst'
used_by:
- description: Phenopackets
id: 'https://github.com/phenopackets/phenopacket-schema/blob/master/docs/family.rst'
sb_status: implemented
properties:
id:
description: An identifier specific for this family
type: string
examples:
- 'family-id-123'
proband:
allof:
- "$ref": https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Phenopacket.json
- description: |
The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient
examples:
- id: 'phenopacketid-123'
metaData:
created: '2016-06-29T12:03:03.240Z'
updates:
- timestamp: '2007-12-03T10:15:30.00Z'
relatives:
description: |
Individuals related in some way to the patient. For instance, the individuals may be genetically related or may
be members of a cohort. If this field is used, then it is expected that a pedigree will be included for
genetically related individuals for use cases such as genomic diagnostics. If a phenopacket is being used to
describe one member of a cohort, then in general one phenopacket will be created for each of the individuals in
the cohort.
type: array
items:
"$ref": https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Phenopacket.json
examples:
- - id: 'phenopacketid-123'
metaData:
created: '2016-06-29T12:03:03.240Z'
updates:
- timestamp: '2007-12-03T10:15:30.00Z'
pedigree:
allof:
- "$ref": https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Pedigree.json
- description: |
The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should
map to the PhenoPacket.Individual.id
examples:
- person:
- individualId: 'add example'
htsFiles:
description: |
Pointer to the relevant HTS file(s) for the family. These should be files relating to one or more of the family
members e.g a multi-sample VCF
type: array
items:
"$ref": https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/HtsFile.json
examples:
- - htsFormat: 'GVCF'
uri: 'file://data/genomes/file1.vcf.gz'
metaData:
allof:
- "$ref": https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/MetaData.json
- description: |
Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED
examples:
- created: '2016-06-29T12:03:03.240Z'
updates:
- timestamp: '2007-12-03T10:15:30.00Z'
required:
- id
- metaData
additionalProperties: false
examples:
- id: 'family-id-123'
proband:
id: 'phenopacketid-123'
metaData:
created: '2016-06-29T12:03:03.240Z'
updates:
- timestamp: '2007-12-03T10:15:30.00Z'
htsFiles:
- htsFormat: 'GVCF'
uri: 'file://data/genomes/file1.vcf.gz'
metaData:
created: '2016-06-29T12:03:03.240Z'
updates:
- timestamp: '2007-12-03T10:15:30.00Z'