BioMetadata: Biosample & Individual

BioMetadata: Biosample Object

Biosample in the GA4GH Schema

The majority of use cases of GA4GH schema compatible resources will serve to facilitate the retrieval of molecular features (DNA sequence variations, gene expression, protein variants) measured by performing experimental (whole genome sequencing, expression arrays, mass spectroscopy) in conjunction with bioinformatics procedures, applied to a preparation of target molecules (e.g. DNA, RNA) which has been extracted from a biological sample (e.g. tissue biopsy, single cell from FACS, environmental sample).

In the GA4GH schema, a Biosample represents the main “biological item” against which molecular variants are referenced.

Biosample attributes

Attribute Notes
id <ul><li>the Biosample’s id</li><li>unique in the context of the server</li><li>used for referencing this Biosample</li></ul>
name <ul><li>a human readable object label/identifier</li><li>not to be used for referencing</li></ul>
description additional, unstructured information about this Biosample
bio_characteristics contains lists of phenotypes, diseases and other information associated with this Biosample, in the form of BioCharacteristic objects
individual_age_at_collection an age object, representing the age of the individual at the time the sample was taken; with information expressed in ISO8601 and/or an ontology class
individualId the id of the Individual this Biosample was derived from
created the time the record was created, in ISO8601
updated the time the record was updated, in ISO8601
attributes additional, structured information
Examples:
Age definition:
"individual_age_at_collection" : {
  "age" : "P6Y0M",
  "age_class" : {
    "term" : "Juvenile onset",
    "term_id" : "HP:0003621"
  }
},
Structured representation of custom attributes:
"attributes" : {
  "tnm" : {
    "values" : [
      {
        "string_value" : "T1N0M0"
      }
    ]
  },
  "death" : {
    "values" : [
      {
        "string_value" : "alive"
      }
    ]
  },

BioMetadata: Individual Object

Individual in the GA4GH Schema

An Individual is a GA4GH data object representing a biological instance (most commonly a human being or other individual organism) on whose Biosamples experimental analyses are performed.

In the case of metagenome analyses (i.e. when the biosample consists of material like patient derived sputum, analyzed for its microbial content), the “species” context would still be the host; identified guest species would be described in analysis results.

Individual attributes

Attribute Notes
id <ul><li>the Individual’s id</li><li>unique in the context of the server</li><li>used for referencing this Individual</li></ul>
name <ul><li>a human readable object label/identifier</li><li>not to be used for referencing</li></ul>
description additional, unstructured information about this Individual
bio_characteristics contains lists of phenotypes, diseases and other information associated with this Individual, in the form of BioCharacteristic objects
species OntologyTerm representing the species (NCBITaxon:9606)
sex OntologyTerm for the genetic sex of this individual.
created the time the record was created, in ISO8601
updated the time the record was updated, in ISO8601
attributes additional, structured information

BioMetadata: BioCharacteristic Object

BioCharacteristic in the GA4GH Schema

A BioCharacteristic is an object, defining a single phenotype or diagnosis through the use of a free text description and a representation by one or more “ontologyTerms” objects as well as zero or more “negatedOntologyTerms”. An additional “scope” attribute allows to limit queries e.g. to “disease” type objects.

Example use:
"bio_characteristics" : [
  {
    "description" : "Diffuse Intrinsic Pontine Glioma",
    "ontology_terms" : [
      {
        "term_label" : "Glioma",
        "term_id" : "ncit:C3059"
      },
      {
        "term_label" : "Glioma NOS",
        "term_id" : "pgx:icdom:9380_3"
      },
      {
        "term_label" : "Brain NOS",
        "term_id" : "pgx:icdot:C71.9"
      }
    ],
    "negated_ontology_terms" : [ ]
  }
],