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=============================
AIRR Community Data Standards
=============================

Introduction
============

One of the core initiatives of the Adaptive Immune Receptor Repertoire
(AIRR) Community [Breden_2017]_ has been to develop standards regarding
the content and format of metadata associated with AIRR sequencing
datasets. The primary aim of this effort is to make published AIRR
datasets `FAIR`_ (findable, accessible, interoperable, reusable). This
work has been a joint effort between the AIRR Community's `Minimal
Standards`_ and `Database Representation`_ Working Groups.

.. _`FAIR`: https://www.force11.org/group/fairgroup/fairprinciples
.. _`Minimal Standards`: http://airr.irmacs.sfu.ca/working_groups/minimal_standards
.. _`Database Representation`: http://airr.irmacs.sfu.ca/node/36


The MiAIRR Data Standard
========================

In order to support FAIR-ness, reproducibility, quality control, and
data deposition in a common repository, the AIRR Community has agreed to
six high-level data sets that will guide the publication, curation and
sharing of AIRR-Seq data and metadata:

- study and subject

- sample collection

- sample processing and sequencing

- raw sequence reads

- processing of sequence data

- processed AIRR sequences

These data sets and their associated individual items are referred to as
**MiAIRR**, the Minimum information about an Adaptive Immune Receptor
Repertoire sequencing experiment. The MiAIRR data standard has recently
been published together with a first implementation using the NCBI
repository structure [Rubelt_2017]_. For further information, including
a submission guide and a detailed specification, see `here`__

.. __: http://docs.airr-community.org/en/latest/miairr/overview.html


Implementations
===============

- `NCBI-based`_
- AIRR Common Repository - _in development_

.. _`NCBI-based`: http://docs.airr-community.org/en/latest/miairr/overview.html



Contributions
=============

The AIRR Community is an open initiative and we welcome all
contributions. Please review our `development process`_ before
contributing changes.

.. _`development process`: https://github.com/airr-community/airr-standards/tree/master/CONTRIBUTING.rst


Build Status
============

.. image:: https://travis-ci.org/airr-community/airr-standards.svg?branch=master
:target: https://travis-ci.org/airr-community/airr-standards

Please report problems, bugs, comments or enhancement requests using
the `issue tracker`_.

.. _`issue tracker`: https://github.com/airr-community/airr-standards/issues
.. https://waffle.io/airr-community/airr-standards
References
==========

.. [Rubelt_2017] Rubelt F *et al*. AIRR Community Recommendations for
Sharing Immune Repertoire Sequencing Data. Nat Immunol 18:1274
(2017) `DOI: 10.1038/ni.3873`_
.. _`DOI: 10.1038/ni.3873`: https://doi.org/10.1038/ni.3873

.. [Breden_2017] Breden F *et al*. Reproducibility and Reuse of
Adaptive Immune Receptor Repertoire Data. Front Immunol 8:1418
(2017) `DOI: 10.3389/fimmu.2017.01418`_
.. _`DOI: 10.3389/fimmu.2017.01418`: https://doi.org/10.3389/fimmu.2017.01418

.. [Zenodo_1185414] Release archive of the AIRR Standards repository.
(2015-2018) `DOI: 10.5281/zenodo.1185414`_
.. _`DOI: 10.5281/zenodo.1185414`: https://doi.org/10.5281/zenodo.1185414


License
=======

.. image:: https://i.creativecommons.org/l/by/4.0/80x15.png
:target: https://creativecommons.org/licenses/by/4.0/

(c) 2015 - 2018 by Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert,
Christian E. Busse, Scott Christley, Brian Corrie, Lindsay G. Cowell,
Uri Hershberg, Steven H. Kleinstein, Frederick A. Matsen IV,
Uri Laserson, Marie-Paule Lefranc, Eline T. Luning Prak, Florian Rubelt,
Jason Vander Heiden, Corey T. Watson

This work is licensed under a `Creative Commons Attribution 4.0
International License`_.

.. _`Creative Commons Attribution 4.0 International License`: http://creativecommons.org/licenses/by/4.0/

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