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

Introduction

One of the core initiatives of the Adaptive Immune Receptor Repertoire (AIRR) Community_ [Breden_2017]_ is to develop and maintain standards regarding the content, format and exchange of data and metadata from AIRR sequencing (AIRR-seq) experiments, thereby contributing to the global endeavor to make scientific data FAIR_ (findable, accessible, interoperable, reusable). The current Standards developed from three initially separate initatives (Minimal Information, Data Representation, API), which converged over time. The further development of the Standards is currently carried out by the AIRR Community's Standards Working Group_ (WG), which was the result of the fusion of the "Data Representation", "Minimal Standards" and parts of the Common Repository_ WGs.

MiAIRR Minimal Information Standard

The Minimal information about an Adaptive Immune Receptor Repertoire (MiAIRR) data standard defines around 60 metadata fields which should be provided to facilitate evaluation and re-use a the data set. These fields are grouped according to the various stage of the typical workflow (e.g., study, subject, sample, experimental processing, data processing, data annotation). MiAIRR was originally published in 2017 [Rubelt_2017]_ and has since been intergrated into the AIRR Data Schema, which has now become the authorative reference for MiAIRR. For further information see the MiAIRR section of the AIRR Standards documentation_.

AIRR Standardized Data Representation

The standardarized data representation was first published in 2018 [Vander_Heiden_2018], the current version of the schema can be found in this repository as OpenAPI v2 and OpenAPI v3_ definitions. The two versions are functionally identical, but users should be aware that support for OpenAPI v2 will be discontinued in the intermediate future.

AIRR Data Commons API

The AIRR Data Commons_ (ADC) API_ [Christley_2020]_ provides programmatic access to query and download AIRR-seq data from ADC repositories.

Implementations

The AIRR Standards are supported by the following services:

• AIRR Data Commons_
• CEDAR-AIRR_

Releases and Issues

Official releases can be found in the release_ section of the repository. There releases are also permanently archived on Zenodo, where they can be referenced to via the archive's DOI [Zenodo_1185414]_.

Contributions

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

References

.. [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]_ .. [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) [PMID:33693395]_ [DOI:10.3389/fdata.2020.00022]_ .. [Lees_2020] Lees W et al. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res 48:D964 (2020) [PMID:31566225]_ [DOI:10.1093/nar/gkz822]_ .. [Lees_2023] Lees W et al. AIRR Community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics 10:100025 (2023) [PMID:37388275]_ [DOI:10.1016/j.immuno.2023.100025]_ .. [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]_ .. [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]_ .. [Zenodo_1185414] Release archive of the AIRR Standards repository. (2018-2022) [DOI:10.5281/zenodo.1185414]_

Copyright & License

Copyright 2015 - 2024 by the AIRR Community and contributors. This work is licensed under a Creative Commons Attribution 4.0 International License.

.. === External links and references ===

.. _[PMID:29144493]: https://www.ncbi.nlm.nih.gov/pubmed/29144493 .. _[PMID:29163494]: https://www.ncbi.nlm.nih.gov/pubmed/29163494 .. _[PMID:30323809]: https://www.ncbi.nlm.nih.gov/pubmed/30323809 .. _[PMID:31566225]: https://www.ncbi.nlm.nih.gov/pubmed/31566225 .. _[PMID:33693395]: https://www.ncbi.nlm.nih.gov/pubmed/33693395 .. _[PMID:37388275]: https://pubmed.ncbi.nlm.nih.gov/37388275 .. _[DOI:10.1038/ni.3873]: https://doi.org/10.1038/ni.3873 .. _[DOI:10.3389/fdata.2020.00022]: https://doi.org/10.3389/fdata.2020.00022 .. _[DOI:10.3389/fimmu.2017.01418]: https://doi.org/10.3389/fimmu.2017.01418 .. _[DOI:10.3389/fimmu.2018.02206]: https://doi.org/10.3389/fimmu.2018.02206 .. _[DOI:10.5281/zenodo.1185414]: https://doi.org/10.5281/zenodo.1185414 .. _[DOI:10.1093/nar/gkz822]: https://doi.org/10.1093/nar/gkz822 .. _[DOI:10.1016/j.immuno.2023.100025]: https://doi.org/10.1016/j.immuno.2023.100025

.. _Adaptive Immune Receptor Repertoire (AIRR) Community: https://www.antibodysociety.org/the-airr-community/ .. _AIRR Data Commons: https://docs.airr-community.org/en/stable/api/adc.html .. _AIRR Data Schema: https://docs.airr-community.org/en/stable/datarep/overview.html#airr-data-model .. _AIRR Standards documentation: https://docs.airr-community.org/en/stable/ .. _API: https://docs.airr-community.org/en/stable/api/adc_api.html .. _CEDAR-AIRR: https://cedar.metadatacenter.org/instances/create/https://repo.metadatacenter.org/templates/ea716306-5263-4f7a-9155-b7958f566933 .. _Common Repository: https://www.antibodysociety.org/the-airr-community/airr-working-groups/repository/ .. _contributors: https://github.com/airr-community/airr-standards/blob/master/CONTRIBUTORS.rst .. _Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0/ .. _development process: https://github.com/airr-community/airr-standards/tree/master/CONTRIBUTING.rst .. _FAIR: https://www.go-fair.org/fair-principles/ .. _issue tracker: https://github.com/airr-community/airr-standards/issues .. _MiAIRR section: https://docs.airr-community.org/en/stable/miairr/introduction_miairr.html .. _OpenAPI v2: https://github.com/airr-community/airr-standards/blob/master/specs/airr-schema.yaml .. _OpenAPI v3: https://github.com/airr-community/airr-standards/blob/master/specs/airr-schema-openapi3.yaml .. _release: https://github.com/airr-community/airr-standards/releases .. _Standards Working Group: https://www.antibodysociety.org/the-airr-community/airr-working-groups/standards/