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One of the core initiatives of the Adaptive Immune Receptor Repertoire (AIRR) Community_ [Breden2017] 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.
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
[Rubelt2017] 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_.
The standardarized data representation was first published in 2018
[Vander_Heiden2018], 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.
The AIRR Data Commons (ADC) API [Christley2020] provides
programmatic access to query and download AIRR-seq data from ADC
repositories.
The AIRR Standards are supported by the following services:
AIRR Data Commons_CEDAR-AIRR_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 [Zenodo1185414].
The AIRR Community is an open initiative and we welcome all
contributions. Please review our development process_ before
contributing changes.
.. [Breden2017] 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]_
.. [Christley2020] 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]_
.. [Lees2020] 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]_
.. [Lees2023] 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]_
.. [Rubelt2017] 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_Heiden2018] 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]_
.. [Zenodo1185414] Release archive of the AIRR Standards repository.
(2018-2022) [DOI:10.5281/zenodo.1185414]
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/