======================
Introduction to MiAIRR
======================

Summary
=======

One of the primary initiatives of the Adaptive Immune Receptor
Repertoire (AIRR) Community has been to develop a set of metadata
standards for the submission of AIRR sequencing datasets. This work has
been carried out by the `AIRR Community Minimal Standards Working Group`_.
In order to support reproducibility, standard 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 sequences, processing
of sequence data, and processed AIRR sequences. The detailed data
elements within these sets are defined here__.

.. _`AIRR Community Minimal Standards Working Group`:
   http://airr-community.org/working_groups/minimal_standards

.. __: https://github.com/airr-community/airr-standards/blob/master/AIRR_Minimal_Standard_Data_Elements.tsv

.. Figure:: images/MiAIRR_data_elements_plain.png
   :alt: A scheme of the MiAIRR data set and data elements
   :figwidth: image

   Schema of MiAIRR data sets and the individual data elements of each
   set.


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

-  NCBI-based - see this document
-  AIRR Common Repositories - *in development*

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