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Journal article
AIRR Community Standardized Representations for Annotated Immune Repertoires
Frontiers in immunology, v 9, pp 2206-2206
28 Sep 2018
PMID: 30323809
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
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.
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Details
- Title
- AIRR Community Standardized Representations for Annotated Immune Repertoires
- Creators
- Jason Anthony Vander Heiden - , , , , , , , , , , , , , , , , , , , , , , , , , ,Susanna Marquez - Yale UniversityNishanth Marthandan - Simon Fraser UniversitySyed Ahmad Chan Bukhari - Yale UniversityChristian E. Busse - German Cancer Research CenterBrian Corrie - Simon Fraser UniversityUri Hershberg - Drexel UniversitySteven H. Kleinstein - Yale UniversityFrederick A. Matsen IV - , , , , , , , , , , , , , , , , , , , , , , , , , ,Duncan K. Ralph - Fred Hutchinson Cancer Research CenterAaron M. Rosenfeld - Drexel UniversityChaim A. Schramm - Vaccine Research CenterScott Christley - Southwestern Medical CenterAIRR CommunityUri Laserson - Icahn School of Medicine at Mount Sinai
- Publication Details
- Frontiers in immunology, v 9, pp 2206-2206
- Publisher
- Frontiers Media S.A
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000445917800001
- Scopus ID
- 2-s2.0-85054889822
- Other Identifier
- 991019167584604721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Immunology