How to cite this record
FAIRsharing.org: AIRR Rearrangement Schema; Adaptive Immune Receptor Repertoire Rearrangement Schema; DOI: https://doi.org/10.25504/FAIRsharing.zwjNAh;
Last edited: Oct. 6, 2020, 11 a.m.; Last accessed: Jan 22 2021 10:56 p.m.
Publication for citation
AIRR Community Standardized Representations for Annotated Immune Repertoires
Vander Heiden JA, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen Iv FA, Ralph DK, Rosenfeld AM, Schramm CA; AIRR Community, Christley S, Laserson U; Frontiers in Immunology ;
2018;
10.3389/fimmu.2018.02206;
Edits to 'https://fairsharing.org/FAIRsharing.zwjNAh' by 'The FAIRsharing Team' at 10:23, 06 Oct 2020 (approved):
'description' has been modified:
Before: The Adaptive Immune Receptor Repertoire Rearrangement Schema defines the annotations needed for rearrangements, which are sequences describing a rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in a tab-delimited file and should be compatible with any TSV reader. A dataset is defined in this context as: a TSV file, a TSV with a companion YAML file containing metadata, or a directory containing multiple TSV files and YAML files.
After: The Adaptive Immune Receptor Repertoire (AIRR) Rearrangement Schema, part of the AIRR Data Model, defines the annotations needed for rearrangements, which are sequences describing a rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in a tab-delimited file and should be compatible with any TSV reader. A dataset is defined in this context as: a TSV file, a TSV with a companion YAML file containing metadata, or a directory containing multiple TSV files and YAML files.
Edits to 'https://fairsharing.org/FAIRsharing.zwjNAh' by 'The FAIRsharing Team' at 10:13, 06 Oct 2020 (approved):
'supportLinks' has been modified:
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online documentation|https://github.com/airr-community/airr-standards
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online documentation|https://github.com/airr-community/airr-standards
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'name' has been modified:
Before: AIRR Rearrangement File Format
After: Adaptive Immune Receptor Repertoire Rearrangement Schema
'licences' has been modified:
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Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
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Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data
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'dataProcesses' has been modified:
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Download Full Schema, data release, https://github.com/airr-community/airr-standards/blob/master/specs/airr-schema.yaml
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Download Full Schema, data release, https://github.com/airr-community/airr-standards/blob/master/specs/airr-schema.yaml
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'shortname' has been modified:
Before: AIRR TSV
After: AIRR Rearrangement Schema
'description' has been modified:
Before: Increased interest in the immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to an explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). The AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of the immune repertoire. In this paper, we describe the work of the AIRR Community's Data Representation Working Group to develop standardized data representations for storing and sharing annotated antibody and T cell receptor data. Our file format emphasizes ease-of-use, accessibility, scalability to large data sets, and a commitment to open and transparent science. It is composed of a tab-delimited format with a specific schema. Several popular repertoire analysis tools and data repositories already utilize this AIRR-seq data format. We hope that others will follow suit in the interest of promoting interoperable standards.
After: The Adaptive Immune Receptor Repertoire Rearrangement Schema defines the annotations needed for rearrangements, which are sequences describing a rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in a tab-delimited file and should be compatible with any TSV reader. A dataset is defined in this context as: a TSV file, a TSV with a companion YAML file containing metadata, or a directory containing multiple TSV files and YAML files.
Edits to 'https://fairsharing.org/FAIRsharing.zwjNAh' by 'The FAIRsharing Team' at 09:53, 06 Oct 2020 (approved):
'homepage' has been modified:
Before: https://docs.airr-community.org/en/stable/datarep/overview.html
After: https://docs.airr-community.org/en/stable/datarep/rearrangements.html
Edits to 'https://fairsharing.org/FAIRsharing.zwjNAh' by 'The FAIRsharing Team' at 07:53, 30 Apr 2020 (approved):
'taxonomies' has been modified:
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All
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All
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'onto_disciplines' has been modified:
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Epidemiology
Immunogenetics
Virology
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Epidemiology
Immunogenetics
Virology
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'related_standards' has been modified:
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Minimal information about Adaptive Immune Receptor Repertoire
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Sequence Alignment Map
Minimal information about Adaptive Immune Receptor Repertoire
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Sequence Alignment Map
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'onto_domains' has been modified:
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T cell receptor complex
immunoglobulin complex, circulating
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T cell receptor complex
immunoglobulin complex, circulating
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'countries' has been modified:
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Worldwide
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Worldwide
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Adaptive Immune Receptor Repertoire Rearrangement Schema
