Abstract
The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is establishing a clear set of community-accepted data and metadata standards; standards-based reference implementation tools; and policies and practices for infrastructure to support the deposit, curation, storage, and use of high-throughput sequencing data from B-cell and T-cell receptor repertoires (AIRR-seq data). The AIRR Data Commons is a distributed system of data repositories that utilizes a common data model, a common query language, and common interoperability formats for storage, query, and downloading of AIRR-seq data. Here is described the principal technical standards for the AIRR Data Commons consisting of the AIRR Data Model for repertoires and rearrangements, the AIRR Data Commons (ADC) API for programmatic query of data repositories, a reference implementation for ADC API services, and tools for querying and validating data repositories that support the ADC API. AIRR-seq data repositories can become part of the AIRR Data Commons by implementing the data model and API. The AIRR Data Commons allows AIRR-seq data to be reused for novel analyses and empowers researchers to discover new biological insights about the adaptive immune system.
Highlights
The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is organizing and coordinating stakeholders in the use of next-generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires (Breden et al, 2017)
The AIRR Data Commons (ADC) API is provided in a machine-readable YAML document that follows the OpenAPI v2.0 specification, and this paper describes Version 1 of the ADC API
Designed to work with the iReceptor Scientific Gateway (Corrie et al, 2018), the iReceptor API provided a set of query mechanisms against AIRR-seq repositories, with an ability to filter both repertoire and rearrangement data in those repositories
Summary
The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is organizing and coordinating stakeholders in the use of next-generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires (Breden et al, 2017). The repertoire endpoint allows querying upon any field in the Repertoire schema including study, subject, sample, cell processing, nucleic acid processing, sequencing run, raw sequencing files, and data processing information. Designed to work with the iReceptor Scientific Gateway (Corrie et al, 2018), the iReceptor API provided a set of query mechanisms against AIRR-seq repositories, with an ability to filter both repertoire and rearrangement data in those repositories. We provide an example use case to demonstrate how to query the ADC API, save the downloaded repertoire and rearrangement data into AIRR standard formatted files, and perform an analysis on the data. This paper describes the AIRR Data Model for repertoires and rearrangements, Version 1 of the ADC API, and standards-based reference implementation tools.
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