Biosample sb-phenopackets

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

Attributes

Type: object
Description: A Biosample refers to a unit of biological material from which the substrate molecules (e.g. genomic DNA, RNA, proteins) for molecular analyses (e.g. sequencing, array hybridisation, mass-spectrometry) are extracted.

Examples would be a tissue biopsy, a single cell from a culture for single cell genome sequencing or a protein fraction from a gradient centrifugation.

Several instances (e.g. technical replicates) or types of experiments (e.g. genomic array as well as RNA-seq experiments) may refer to the same Biosample.

FHIR mapping: Specimen.

Properties

Property Type
ageOfIndividualAtCollection https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Age.json [SRC] [HTML]
ageRangeOfIndividualAtCollection https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/AgeRange.json [SRC] [HTML]
description string
diagnosticMarkers array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]"
histologicalDiagnosis https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
htsFiles array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/HtsFile.json [SRC] [HTML]"
id string
individualId string
isControlSample boolean
phenotypicFeature array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/PhenotypicFeature.json [SRC] [HTML]"
procedure https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Procedure.json [SRC] [HTML]
sampledTissue https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
taxonomy https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
tumorGrade https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
tumorProgression https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
variants array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Variant.json [SRC] [HTML]"

ageOfIndividualAtCollection

An age object describing the age of the individual this biosample was derived from at the time of collection. The Age object allows the encoding of the age either as ISO8601 duration or time interval (preferred), or as ontology term object. See http://build.fhir.org/datatypes

ageOfIndividualAtCollection Value Example
{
   "age" : "P48Y3M"
}

ageRangeOfIndividualAtCollection

An age range object describing the age of the individual this biosample was derived from at the time of collection. The Age object allows the encoding of the age either as ISO8601 duration or time interval (preferred), or as ontology term object. See http://build.fhir.org/datatypes

ageRangeOfIndividualAtCollection Value Example
{
   "end" : {
      "age" : "P18Y"
   },
   "start" : {
      "age" : "P12Y"
   }
}

description

The biosample’s description. This attribute contains human readable text. The “description” attributes should not contain any structured data.

description Value Example
"THP-1; 6 hours; DMSO; Replicate 1"

diagnosticMarkers

Clinically relevant bio markers. Most of the assays such as IHC are covered by the NCIT under the sub-hierarchy NCIT:C25294 (Laboratory Procedure). e.g. NCIT:C68748 (HER2/Neu Positive), NCIT:C131711 (Human Papillomavirus-18 Positive)

diagnosticMarkers Value Example
[
   {
      "id" : "NCIT:C131711",
      "label" : "Human Papillomavirus-18 Positive"
   }
]

histologicalDiagnosis

This is the pathologist’s diagnosis and may often represent a refinement of the clinical diagnosis given in the Patient/Clinical module. Should use the same terminology as diagnosis, but represent the pathologist’s findings. Normal samples would be tagged with the term “NCIT:C38757”, “Negative Finding”

histologicalDiagnosis Value Example
{
   "id" : "EFO:0000221",
   "label" : "Acute Monocytic Leukemia"
}

htsFiles

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

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

id

The local-unique identifier of this biosample (referenced as “biosample_id”). This is unique in the context of the local (e.g. server, resource) instance.

id Value Example
"SAMN05324082"

individualId

In a complete data model “individual_id” points to the “id” of the individual (“donor”, “subjerct”…) this Biosample was derived from.

In a local context this could be the id attribute in a corresponding “individuals” collection.

individualId Value Example
"SAMN05324082-individual"

isControlSample

if true, this sample is being use as a normal control, often in combination with another sample that is thought to contain a pathological finding the default value is false

isControlSample Value Example
""

phenotypicFeature

Phenotypic characteristics of the BioSample, for example histological findings of a biopsy

phenotypicFeature Value Example
[
   {
      "type" : {
         "id" : "EFO:0001253",
         "label" : "THP-1"
      }
   }
]

procedure

Clinical procedure performed on the subject in order to extract the biosample.

procedure Value Example
{
   "bodySite" : {
      "id" : "UBERON:0003403",
      "label" : "skin of forearm"
   },
   "code" : {
      "id" : "NCIT:C28743",
      "label" : "Funch Biopsy"
   }
}

sampledTissue

UBERON class describing the tissue from which the specimen was collected. PDX-MI mapping: ‘Specimen tumor tissue’ FHIR mapping: Specimen.type

sampledTissue Value Example
{
   "id" : "UBERON:0000178",
   "label" : "peripheral blood"
}

taxonomy

NCBI taxonomic identifier (NCBITaxon) of the sample e.g. NCBITaxon:9606

taxonomy Value Example
{
   "description" : "Homo sapiens",
   "type" : "NCBITaxon:9606"
}

tumorGrade

Potentially a child term of NCIT:C28076 (Disease Grade Qualifier) or equivalent See https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet

tumorGrade Value Example
{
   "id" : "NCIT:C28091",
   "label" : "Gleason Score 7"
}

tumorProgression

Is the specimen tissue from the primary tumor, a metastasis or a recurrence? Most likely a child term of NCIT:C7062 (Neoplasm by Special Category) NCIT:C3677 (Benign Neoplasm) NCIT:C84509 (Primary Malignant Neoplasm) NCIT:C95606 (Second Primary Malignant Neoplasm) NCIT:C3261 (Metastatic Neoplasm) NCIT:C4813 (Recurrent Malignant Neoplasm)

tumorProgression Value Example
{
   "id" : "NCIT:C84509",
   "label" : "Primary Malignant Neoplasm"
}

variants

Field for variants relevant to this biosample

variants Value Example
[
   {
      "background" : "add example",
      "hgvsAllele" : "add example"
   }
]

Biosample Value Examples

{
   "ageOfIndividualAtCollection" : {
      "age" : "P1Y"
   },
   "description" : "THP-1; 6 hours; DMSO; Replicate 1",
   "histologicalDiagnosis" : {
      "id" : "EFO:0000221",
      "label" : "Acute Monocytic Leukemia"
   },
   "id" : "SAMN05324082",
   "individualId" : "SAMN05324082-individual",
   "phenotypicFeature" : [
      {
         "type" : {
            "id" : "EFO:0001253",
            "label" : "THP-1"
         }
      }
   ],
   "sampledTissue" : {
      "id" : "UBERON:0000178",
      "label" : "peripheral blood"
   },
   "taxonomy" : {
      "id" : "NCBITaxon:9606",
      "label" : "Homo sapiens"
   }
}
{
   "ageOfIndividualAtCollection" : {
      "age" : "P1Y"
   },
   "diagnosticMarkers" : [
      {
         "id" : "NCIT:C131711",
         "label" : "Human Papillomavirus-18 Positive"
      }
   ],
   "histologicalDiagnosis" : {
      "id" : "EFO:0000221",
      "label" : "Acute Monocytic Leukemia"
   },
   "id" : "SAMN05324083",
   "individualId" : "SAMN05324083-individual",
   "procedure" : {
      "code" : {
         "id" : "NCIT:C15189",
         "label" : "Biopsy"
      }
   },
   "sampledTissue" : {
      "id" : "NCIT:C139196",
      "label" : "Esophageal Lymph Node"
   },
   "tumorProgression" : {
      "id" : "NCIT:C84509",
      "label" : "Primary Malignant Neoplasm"
   },
   "tumorStage" : [
      {
         "id" : "NCIT:C48724",
         "label" : "T2 Stage Finding"
      },
      {
         "id" : "NCIT:C48706",
         "label" : "N1 Stage Finding"
      },
      {
         "id" : "NCIT:C48699",
         "label" : "M0 Stage Finding"
      }
   ]
}