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============================= | ||
AIRR Community Data Standards | ||
============================= | ||
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Introduction | ||
============ | ||
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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. | ||
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.. _`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 | ||
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The MiAIRR Data Standard | ||
======================== | ||
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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: | ||
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- study and subject | ||
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- sample collection | ||
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- sample processing and sequencing | ||
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- raw sequence reads | ||
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- processing of sequence data | ||
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- processed AIRR sequences | ||
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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`__ | ||
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.. __: http://docs.airr-community.org/en/latest/miairr/overview.html | ||
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Implementations | ||
=============== | ||
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- `NCBI-based`_ | ||
- AIRR Common Repository - _in development_ | ||
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.. _`NCBI-based`: http://docs.airr-community.org/en/latest/miairr/overview.html | ||
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Contributions | ||
============= | ||
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The AIRR Community is an open initiative and we welcome all | ||
contributions. Please review our `development process`_ before | ||
contributing changes. | ||
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.. _`development process`: https://github.com/airr-community/airr-standards/tree/master/CONTRIBUTING.rst | ||
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Build Status | ||
============ | ||
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.. image:: https://travis-ci.org/airr-community/airr-standards.svg?branch=master | ||
:target: https://travis-ci.org/airr-community/airr-standards | ||
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Please report problems, bugs, comments or enhancement requests using | ||
the `issue tracker`_. | ||
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.. _`issue tracker`: https://github.com/airr-community/airr-standards/issues | ||
.. https://waffle.io/airr-community/airr-standards | ||
References | ||
========== | ||
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.. [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 | ||
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.. [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 | ||
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.. [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 | ||
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License | ||
======= | ||
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.. image:: https://i.creativecommons.org/l/by/4.0/80x15.png | ||
:target: https://creativecommons.org/licenses/by/4.0/ | ||
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(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 | ||
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This work is licensed under a `Creative Commons Attribution 4.0 | ||
International License`_. | ||
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.. _`Creative Commons Attribution 4.0 International License`: http://creativecommons.org/licenses/by/4.0/ |