Adaptive Immune Receptor Repertoire Rearrangement Schema
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Adaptive Immune Receptor Repertoire Rearrangement Schema
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
AIRR Rearrangement Schema
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
Names
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Adaptive Immune Receptor Repertoire Rearrangement Schema
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
AIRR Rearrangement Schema
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
Other names: AIRR Rearrangement Schema
Names
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Adaptive Immune Receptor Repertoire Rearrangement Schema
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
AIRR Rearrangement Schema
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
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.
Description
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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.
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
Webpage:
https://docs.airr-community.org/en/stable/datarep/rearrangements.htmlWebpage
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https://docs.airr-community.org/en/stable/datarep/rearrangements.html
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
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Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
Licence URL
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https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
Publications:
Publications
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AIRR Community Standardized Representations for Annotated Immune Repertoires
PMID: 30323809
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
Publications
More detailed information about this field from each metasource.
AIRR Community Standardized Representations for Annotated Immune Repertoires
PMID: 30323809
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
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AIRR Community Standardized Representations for Annotated Immune Repertoires
PubMed citations: 21.
21 articles citing: AIRR Community Standardized Representations for Annotated Immune Repertoires
Machine Learning Approaches to TCR Repertoire Analysis. PMID:35911778
Data Sharing and Reuse: A Method by the AIRR Community. PMID:35622339
Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community. PMID:35622334
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information. PMID:35325179
Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire. PMID:35003093
T-Cell Receptor Repertoire Analysis with Computational Tools-An Immunologist's Perspective. PMID:34944090
High-throughput and single-cell T cell receptor sequencing technologies. PMID:34282327
Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. PMID:34037521
Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls. PMID:33790900
The Future of Blood Testing Is the Immunome. PMID:33790897
The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. PMID:33693395
The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data. PMID:33073065
Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation? PMID:32853330
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. PMID:32614448
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PMID:32574157
Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma. PMID:32134923
Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads. PMID:32109676
Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. PMID:31906351
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. PMID:31873728
sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation. PMID:31736960
cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence. PMID:31649674
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antibody
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
t cell receptor complex
metasource: Fairsharing.org
version: 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 03 2022 7:14 p.m.
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antibody
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
t cell receptor complex
metasource: Fairsharing.orgversion: 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 03 2022 7:14 p.m.
antibody t cell receptor complex
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