tandreanisanofi / airr-standards

AIRR Community Data Standards

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 Data Representation Working Groups.

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 the respective section of the AIRR Standards documentation.

AIRR Standardized Data Representation

The standardarized data representation was first published in 2018 [Vander_Heiden_2018], a current version of the schema can be found here.

AIRR Data Commons API

The AIRR Data Commons (ADC) API was published in 2020 [Christley_2020].

Implementations

• NCBI-based
• AIRR Common Repository - in development

Contributions

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

Build Status, Issues and Archive

Please report problems, bugs, comments or enhancement requests using the issue tracker. Official releases are archived and DOI referenced via Zenodo [Zenodo_1185414].

References

License

(c) 2015 - 2020 by Francisco Arcila, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Christian E. Busse, Scott Christley, Brian Corrie, Lindsay G. Cowell, Srilakshmy L. Harikrishnan, Uri Hershberg, Steven H. Kleinstein, Susanna Marquez, 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.

Breden_2017

Breden F et al. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 8:1418 (2017) [PMID: 29163494] [DOI: 10.3389/fimmu.2017.01418] [PubMed Central: PMC5671925]

Christley_2020

Christley S et al. The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Front Big Data (2020) [DOI: 10.3389/fdata.2020.00022]

Rubelt_2017

Rubelt F et al. AIRR Community Recommendations for Sharing Immune Repertoire Sequencing Data. Nat Immunol 18:1274 (2017) [PMID: 29144493] [DOI: 10.1038/ni.3873] [PubMed Central: PMC5790180]

Vander_Heiden_2018

Vander Heiden JA et al. AIRR Community Standardized Representations for Annotated Immune Repertoires. Front Immunol 9:2206 (2018) [PMID: 30323809] [DOI: 10.3389/fimmu.2018.02206] [PubMed Central: PMC6173121]

Zenodo_1185414

Release archive of the AIRR Standards repository. (2015-2020) [DOI: 10.5281/zenodo.1185414]