diff --git a/README.md b/README.md deleted file mode 100644 index d10c5d3df..000000000 --- a/README.md +++ /dev/null @@ -1,83 +0,0 @@ -![Image](https://github.com/airr-community/airr-standards/raw/master/images/miairr_logo.png) - -_Minimum information about an Adaptive Immune Receptor Repertoire Sequencing Experiment_ - -*** - -### Introduction -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](http://airr.irmacs.sfu.ca/working_groups/minimal_standards). 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](https://github.com/airr-community/airr-standards/blob/master/AIRR_Minimal_Standard_Data_Elements.tsv). - -### Implementations - -- [NCBI-based](http://docs.airr-community.org/en/latest/miairr/miairr_ncbi_overview.html) -- AIRR Common Repositories - _in development_ - -### References - -Rubelt F _et al._ -Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. -Nat Immunol 18:1274 (2017) -[[PubMed]](https://www.ncbi.nlm.nih.gov/pubmed/29144493) [[DOI]](https://doi.org/10.1038/ni.3873) [[SharedIt - free to read]](https://rdcu.be/E7sS) - -Breden F _et al._ -Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. -Front Immunol 8:1418 (2017) -[[PubMed]](https://www.ncbi.nlm.nih.gov/pubmed/29163494) [[DOI]](https://doi.org/10.3389/fimmu.2017.01418) - - - -*** -### How to contribute? - -The AIRR Community is an open initiative and we welcome all contributions. Please review our -[development process](https://github.com/airr-community/airr-standards/tree/master/CONTRIBUTING.md) -before contributing changes. - -### Report an issue to help us improving MiAIRR - -[![Build Status](https://travis-ci.org/airr-community/airr-standards.svg?branch=master)](https://travis-ci.org/airr-community/airr-standards) - -https://waffle.io/airr-community/airr-standards - -### Contact - -For further information about the MiAIRR standard please contact -[Syed **Ahmad** Chan Bukhari](mailto:ahmad.chan@yale.edu?subject=MiAIRR%20Standard) or -[Steven Kleinstein](mailto:steven.kleinstein@yale.edu?subject=MiAIRR%20Standard). - -*** -### License - -(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 - -[![Image](https://i.creativecommons.org/l/by/4.0/80x15.png)](http://creativecommons.org/licenses/by/4.0/) -This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/). - -*** -### Share on Social Media - -[![alt text][1.1]][1] -[![alt text][2.1]][2] -[![alt text][3.1]][3] - -[1.1]: http://i.imgur.com/tXSoThF.png (twitter icon with padding) -[2.1]: http://i.imgur.com/P3YfQoD.png (facebook icon with padding) -[3.1]: http://i.imgur.com/yCsTjba.png (google plus icon with padding) - -[1]: https://twitter.com/share?url=https://github.com/airr-community/airr-standards -[2]: https://www.facebook.com/sharer/sharer.php?u=https://github.com/airr-community/airr-standards -[3]: https://plus.google.com/share?url=https://github.com/airr-community/airr-standards diff --git a/README.rst b/README.rst new file mode 100644 index 000000000..72512bfd5 --- /dev/null +++ b/README.rst @@ -0,0 +1,117 @@ +============================= +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/