Family sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

Type: object
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

Properties

Property Type
htsFiles array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/HtsFile.json [SRC] [HTML]"
id string
metaData https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/MetaData.json [SRC] [HTML]
pedigree https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Pedigree.json [SRC] [HTML]
proband https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Phenopacket.json [SRC] [HTML]
relatives array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Phenopacket.json [SRC] [HTML]"

htsFiles

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

htsFiles Value Example
[
   {
      "htsFormat" : "GVCF",
      "uri" : "file://data/genomes/file1.vcf.gz"
   }
]

id

An identifier specific for this family

id Value Example
"family-id-123"

metaData

Structured definitions of the resources and ontologies used within the phenopacket. REQUIRED

metaData Value Example
{
   "created" : "2016-06-29T12:03:03.240Z",
   "updates" : [
      {
         "timestamp" : "2007-12-03T10:15:30.00Z"
      }
   ]
}

pedigree

The pedigree defining the relations between the proband and their relatives. Pedigree.individual_id should map to the PhenoPacket.Individual.id

pedigree Value Example
{
   "person" : [
      {
         "individualId" : "add example"
      }
   ]
}

proband

The individual representing the focus of this packet - e.g. the proband in rare disease cases or cancer patient

proband Value Example
{
   "id" : "phenopacketid-123",
   "metaData" : {
      "created" : "2016-06-29T12:03:03.240Z",
      "updates" : [
         {
            "timestamp" : "2007-12-03T10:15:30.00Z"
         }
      ]
   }
}

relatives

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.

relatives Value Example
[
   {
      "id" : "phenopacketid-123",
      "metaData" : {
         "created" : "2016-06-29T12:03:03.240Z",
         "updates" : [
            {
               "timestamp" : "2007-12-03T10:15:30.00Z"
            }
         ]
      }
   }
]

Family Value Example

{
   "htsFiles" : [
      {
         "htsFormat" : "GVCF",
         "uri" : "file://data/genomes/file1.vcf.gz"
      }
   ],
   "id" : "family-id-123",
   "metaData" : {
      "created" : "2016-06-29T12:03:03.240Z",
      "updates" : [
         {
            "timestamp" : "2007-12-03T10:15:30.00Z"
         }
      ]
   },
   "proband" : {
      "id" : "phenopacketid-123",
      "metaData" : {
         "created" : "2016-06-29T12:03:03.240Z",
         "updates" : [
            {
               "timestamp" : "2007-12-03T10:15:30.00Z"
            }
         ]
      }
   }
}