bio_metadata

An individual (or subject) typically corresponds to an individual human or another organism.

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. In the context of the GA4GH metadata schema, Biosample constitutes the central reference object.

message Individual
Fields:
  • id (string) – The Individual’s id. This is unique in the context of the server instance.
  • dataset_id (string) – The ID of the dataset this Individual belongs to.
  • name (string) – The Individual’s name. This is a label or symbolic identifier for the individual.
  • description (string) – The Individual’s description. This attribute contains human readable text. The “description” attributes should not contain any structured data.
  • created (string) – The ISO 8601 time at which this Individual’s record was created.
  • updated (string) – The ISO 8601 time at which this Individual record was updated.
  • species (OntologyTerm) – For a representation of an NCBI Taxon ID as an OntologyTerm, see NCBITaxon Ontology http://www.obofoundry.org/ontology/ncbitaxon.html For example, ‘Homo sapiens’ has the ID 9606. The NCBITaxon ontology ID for this is NCBITaxon:9606, which has the URI http://purl.obolibrary.org/obo/NCBITaxon_9606
  • sex (OntologyTerm) – The genetic sex of this individual. Use null when unknown or not applicable. Recommended: PATO http://purl.obolibrary.org/obo/PATO_0020001; PATO_0020002
  • attributes (Attributes) – A map of additional information regarding the Individual.
message Biosample
Fields:
  • id (string) – The Biosample id. This is unique in the context of the server instance.
  • dataset_id (string) – The ID of the dataset this Biosample belongs to.
  • name (string) – The Biosample’s name This is a label or symbolic identifier for the biosample.
  • description (string) – The biosample’s description. This attribute contains human readable text. The “description” attributes should not contain any structured data.
  • disease (OntologyTerm) – OntologyTerm describing the primary disease associated with this Biosample.
  • created (string) – The ISO 8601 time at which this Biosample record was created.
  • updated (string) – The ISO 8601 time at which this Biosample record was updated.
  • individual_id (string) – The individual this biosample was derived from.
  • attributes (Attributes) – A map of additional information about the Biosample.