The API is designed for sharing genomic data. It currently has support for sharing sequencing reads, genetic variants, and reference genomes. The following sections give an overview of the API, including general API patterns, individual data types, and links to detailed schema documentation.
Reads are genetic data generated by a DNA sequencing instrument, including nucleotides and quality scores. Reads may optionally be aligned to a reference sequence. (The data model for reads is similar to SAM/BAM.)
Variants are genetic differences between an experimental sample and a reference sequence. (The data model for variants is similar to VCF.)
References are standard genome sequences, used to provide a coordinate system for reads and variants.
Sequence annotations describe genomic features such as genes and exons, using terms from an established sequence ontology.
Metadata allows organizing all the primary data types.
- Metadata API
- BioMetadata: Biosample Object
- BioMetadata: Individual Object
- AssayMetadata: Experiment Object
- AssayMetadata: Analysis Object
Allele annotations are additional pieces of data often generated by algorithms which help to describe, classify, and understand variants.
The RNA quantifications provides a means of obtaining feature level quantifications derived from a set of RNA reads.
Genotype to Phenotype¶
Genotype and phenotype data can be linked via evidence. This protocol provides methods for describing phenotypes and associating them with genomic features.
- Genotype To Phenotype API
- Multiple server collation - Background
- Data Model
- API Details and Examples
- Use cases
- Directions for future capabilities.
GA4GH services can communicate with each other about the services they offer over network protocols. This includes the Peer Service.