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.

The age object permits both the (considered default) encoding of an age value in ISO8601, with arbitrary granularity; and the representation of an “age class” as qualitative ontology term. If available, a quantitative value should be used & take precedence over the age class, and class assignment should be performed at user/API level.

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, and therefore: species : { term_id: “NCBITaxon:9606”, term : “Homo sapiens” }
  • sex (OntologyTerm) – The genetic sex of this individual. Use null when unknown or not applicable. Recommended: PATO http://purl.obolibrary.org/obo/PATO_0020000 … Example: sex : { term_id: “PATO:0020000”, term : “female genetic sex” }
  • 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.
  • individual_age_at_collection (Age) – 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 duraion or time interval (preferred), or as ontology term object.
message Age
Fields:
  • age (string) – The ISO 8601 age of this object as ISO8601 duration or time intervals. The use of time intervals makes an additional anchor unnecessary (i.e. DOB and age can be represented as start-anchored time interval, e.g. 1967-11-21/P40Y10M05D) TODO: Anonymous reference time attribute/pointer?
  • age_class (OntologyTerm) – An age class, e.g. corresponding to the use of “age of onset” in HPO. HPO is recommended, for example, subclasses of http://purl.obolibrary.org/obo/HP_0003674 Example: age_class : { term_id : “HP:0003596”, term : “Middle age onset” }