Phenopacket sb-phenopackets

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

Attributes

Type: object
Description: An anonymous phenotypic description of an individual or biosample with potential genes of interest and/or diagnoses. This is a bundle of high-level concepts with no specifically defined relational concepts. It is expected that the resources sharing the phenopackets will define and enforce their own semantics and level of requirements for included fields.

Properties

Property Type
biosamples array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Biosample.json [SRC] [HTML]"
diseases array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Disease.json [SRC] [HTML]"
genes array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Gene.json [SRC] [HTML]"
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]
phenotypicFeatures array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/PhenotypicFeature.json [SRC] [HTML]"
subject https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Individual.json [SRC] [HTML]
variants array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Variant.json [SRC] [HTML]"

biosamples

Biosample(s) derived from the patient or a collection of biosamples in isolation

biosamples Value Example
[
   {
      "description" : "THP-1; 6 hours; DMSO; Replicate 1",
      "id" : "SAMN05324082",
      "individualId" : "SAMN05324082-individual",
      "sampledTissue" : {
         "id" : "UBERON:0000178",
         "label" : "peripheral blood"
      }
   }
]

diseases

Field for disease identifiers - could be used for listing either diagnosed or suspected conditions. The resources using these fields should define what this represents in their context.

diseases Value Example
[
   {
      "classOfOnset" : {
         "id" : "HP:0003596",
         "label" : "Middle age onset"
      },
      "term" : {
         "id" : "MONDO:0007043",
         "label" : "Pfeiffer syndrome"
      }
   }
]

genes

Field for gene identifiers - could be used for listing either candidate genes or causative genes. The resources using these fields should define what this represents in their context. This could be used in order to obfuscate the specific causative/candidate variant.

genes Value Example
[
   {
      "id" : "HGNC:3477",
      "symbol" : "ETF1"
   }
]

htsFiles

Pointer to the relevant HTS file(s) for the patient

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

id

An identifier specific for this phenopacket

id Value Example
"phenopacketid123"

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"
      }
   ]
}

phenotypicFeatures

Phenotypic features relating to the subject of the phenopacket

phenotypicFeatures Value Example
[
   {
      "description" : "add example",
      "type" : {
         "id" : "add example",
         "label" : "add example"
      }
   }
]

subject

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

subject Value Example
{
   "id" : "SAMN05324082-individual",
   "sex" : "MALE",
   "taxonomy" : {
      "id" : "NCBITaxon:9606",
      "label" : "Homo sapiens"
   }
}

variants

Field for genetic variants - could be used for listing either candidate variants or diagnosed causative variants. The resources using these fields should define what this represents in their context.

variants Value Example
[
   {
      "description" : "description of variant",
      "id" : "ID_12345",
      "murineAllele" : {
         "alleleSymbol" : "tm1Hcd",
         "gene" : "Fbn1",
         "id" : "MGI:3690325"
      }
   }
]

Phenopacket Value Example

{
   "biosamples" : [
      {
         "description" : "THP-1; 6 hours; DMSO; Replicate 1",
         "id" : "SAMN05324082",
         "individualId" : "SAMN05324082-individual",
         "sampledTissue" : {
            "id" : "UBERON:0000178",
            "label" : "peripheral blood"
         }
      }
   ],
   "id" : "phenopacketid-123",
   "metaData" : {
      "created" : "2016-06-29T12:03:03.240Z",
      "updates" : [
         {
            "timestamp" : "2007-12-03T10:15:30.00Z"
         }
      ]
   },
   "subject" : {
      "id" : "SAMN05324082-individual",
      "sex" : "MALE",
      "taxonomy" : {
         "id" : "NCBITaxon:9606",
         "label" : "Homo sapiens"
      }
   }
}