.. _DataCommons:

AIRR Data Commons
=============================

The use of high-throughput sequencing for profiling B-cell and T-cell
receptors has resulted in a rapid increase in data generation. It is
timely, therefore, for the Adaptive Immune Receptor Repertoire (AIRR)
community to establish a clear set of community-accepted data and
metadata standards; analytical tools; and policies and practices for
infrastructure to support data deposit, curation, storage, and
use. Such actions are in accordance with international funder and
journal policies that promote data deposition and data sharing – at a
minimum, data on which scientific publications are based should be
made available immediately on publication. Data deposit in publicly
accessible databases ensures that published results may be
validated. Such deposition also facilitates reuse of data for the
generation of new hypotheses and new knowledge.

The AIRR Common Repository Working Group (CRWG) has developed a set of
recommendations__ that promote the deposit, sharing, and use
of AIRR sequence data. These recommendations were refined following
community discussions at the AIRR 2016 and 2017 Community Meetings and
were approved through a vote by the AIRR Community at the AIRR
Community Meeting in December 2017. Updates to these recommendations have continued,
with the latest set of Recommendations ratified at the AIRR Community meeting in May 2019.

In May 2020, the AIRR Community released the first verion of the AIRR Data Commons
Application Programming Interface (ADC API), a specification for programmatic access to
query and download AIRR-seq data from repositories that adhere to the AIRR Standards. We define 
the AIRR Data Commons as consisting of the set of repositories that:

- adhere to the CRWG recommendations for promoting, sharing, and use of AIRR-seq data, and
- that implement the ADC API as a programmatic mechanism to access that data.

This page provides a central location for the community to discover resources that belong to the
AIRR Data Commons.

.. __: https://github.com/airr-community/common-repo-wg/blob/master/recommendations.md

AIRR Data Commons Repositories
---------------------------------------

The repositories that are part of the ADC are listed on the `AIRR Community ADC Registry github site 
<https://github.com/airr-community/adc-registry/blob/ADC/ADC-registry.tsv>`_. In order
to find data across all of the repositories in the ADC, it is necessary to query all of these repositories.

Querying the AIRR Data Commons
---------------------------------------

Each of the repositories above can be queried directly using the :ref:`ADC API <DataCommonsAPI>`. In addition, the
following tools and platforms implement web based user interfaces that use the ADC API to query repositories
in the AIRR Data Commons:

+ :ref:`iReceptor Gateway <iReceptor>`
+ :ref:`VDJServer Community Data Portal <VDJServer>`

There are :ref:`query and analysis use cases <DataCommonsExample>` and
:ref:`a set of example queries <DataCommonsQueries>` available for the
AIRR Data Commons and the ADC API.