Biosample progenetix

{S}[B] Status [i]
external
Provenance
Used by
Contributors
Source (v2020-02-12)

Attributes

Type: object
Description: In this schema, a “biosample” as the source of the material of a molecular analysis (e.g. genomic array, sequencing), represents the main “biological item” against which molecular variants are referenced.

Properties

Property Type
age_at_collection https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Age.json [SRC] [HTML]
biocharacteristics array of ./ExtendedClass.json [SRC] [HTML]
created string
data_use_conditions https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
description string
external_references array of ./ExtendedClass.json [SRC] [HTML]
id string
individualId string
info ./Info.json [SRC] [HTML]
provenance ./ProvenanceClass.json [SRC] [HTML]
updated string

age_at_collection

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

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

biocharacteristics

“biocharacteristics” represents a wrapper list of “ExtendedClass” objects with properly prefixed term ids, describing features of the biosample. Examples would be phenotypes, disease codes or other ontology classes specific to this biosample. In a complete data model (variants - (callsets) - biosamples - individuals), characteristics applying to the individual (e.g. sex, most phenotypes) should be annotated there.

biocharacteristics Value Example
[
   {
      "class" : {
         "id" : "icdot:C25.9",
         "label" : "Pancreas, NOS"
      },
      "description" : "Pancreatic Adenocarcinoma"
   },
   {
      "class" : {
         "id" : "icdom:81403",
         "label" : "Adenocarcinoma, NOS"
      },
      "description" : "Pancreatic Adenocarcinoma"
   },
   {
      "class" : {
         "id" : "ncit:C8294",
         "label" : "Pancreatic Adenocarcinoma"
      },
      "description" : "Pancreatic Adenocarcinoma"
   }
]

created

The creation time of this record, in ISO8601

created Value Example

data_use_conditions

Data use conditions applying to data from this biosample, as ontology object (e.g. DUO).

data_use_conditions Value Example
{
   "id" : "DUO:0000004",
   "label" : "no restriction"
}

description

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

description Value Example
"Burkitt lymphoma, cell line Namalwa"

external_references

list of reference_class objects with properly (e.g. identifiers.org) prefixed external identifiers and a term describing the relationship

external_references Value Example
[
   {
      "description" : "Human Bone Osteosarcoma cell line",
      "type" : {
         "id" : "cellosaurus:CVCL_0312",
         "label" : "HOS"
      }
   },
   {
      "description" : "Article: Greshock et al.: Cancer cell lines as genetic models of their parent histology",
      "relation" : "report",
      "type" : {
         "id" : "PMID:17440070"
      }
   }
]

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"

info

This is a wrapper for objects without further specification in the schema.

info Value Example
[
   {
      "death" : "1",
      "followup_time" : "P14M"
   }
]

provenance

Aspects such as geographic origin or material type, processing, providing additional information about the biosample.

provenance Value Example
[
   {
      "geo" : {
         "city" : "New York City",
         "country" : "United States",
         "geojson" : {
            "coordinates" : [
               "74.01",
               "40.71"
            ],
            "type" : "Point"
         },
         "label" : "New York City, United States",
         "latitude" : "40.71",
         "longitude" : "-74.01",
         "precision" : "city"
      },
      "material" : {
         "description" : "normal cervix",
         "type" : {
            "id" : "EFO:0009654",
            "label" : "reference sample"
         }
      }
   }
]

updated

The time of the last edit of this record, in ISO8601

updated Value Example

Biosample Value Example

2020-03-28