The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories
The adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of ada...
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Frontiers Media S.A.
2018-08-01
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Series: | Frontiers in Immunology |
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Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2018.01877/full |
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doaj-e28f95a5137843d3a78e695d29ec81b2 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Syed Ahmad Chan Bukhari Martin J. O’Connor Marcos Martínez-Romero Attila L. Egyedi Debra Willrett John Graybeal Mark A. Musen Florian Rubelt Kei-Hoi Cheung Kei-Hoi Cheung Kei-Hoi Cheung Steven H. Kleinstein Steven H. Kleinstein |
spellingShingle |
Syed Ahmad Chan Bukhari Martin J. O’Connor Marcos Martínez-Romero Attila L. Egyedi Debra Willrett John Graybeal Mark A. Musen Florian Rubelt Kei-Hoi Cheung Kei-Hoi Cheung Kei-Hoi Cheung Steven H. Kleinstein Steven H. Kleinstein The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories Frontiers in Immunology immune-repertoire sequencing Rep-seq antibody B cell receptor T cell receptor National Center for Biotechnology Information |
author_facet |
Syed Ahmad Chan Bukhari Martin J. O’Connor Marcos Martínez-Romero Attila L. Egyedi Debra Willrett John Graybeal Mark A. Musen Florian Rubelt Kei-Hoi Cheung Kei-Hoi Cheung Kei-Hoi Cheung Steven H. Kleinstein Steven H. Kleinstein |
author_sort |
Syed Ahmad Chan Bukhari |
title |
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories |
title_short |
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories |
title_full |
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories |
title_fullStr |
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories |
title_full_unstemmed |
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories |
title_sort |
cairr pipeline for submitting standards-compliant b and t cell receptor repertoire sequencing studies to the national center for biotechnology information repositories |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Immunology |
issn |
1664-3224 |
publishDate |
2018-08-01 |
description |
The adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses. However, effective sharing of these large-scale data remains a challenge. The AIRR community has proposed minimal information about adaptive immune receptor repertoire (MiAIRR), a standard for reporting AIRR-seq studies. The MiAIRR standard has been operationalized using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientists’ ability to access, find, interoperate, and reuse the data sets. In order to improve metadata quality and ease submission of AIRR-seq studies to the NCBI, we have leveraged the software framework developed by the Center for Expanded Data Annotation and Retrieval (CEDAR), which develops technologies involving the use of data standards and ontologies to improve metadata quality. The resulting CEDAR-AIRR (CAIRR) pipeline enables data submitters to: (i) create web-based templates whose entries are controlled by ontology terms, (ii) generate and validate metadata, and (iii) submit the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive databases. Overall, CAIRR provides a web-based metadata submission interface that supports compliance with the MiAIRR standard. This pipeline is available at http://cairr.miairr.org, and will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies. |
topic |
immune-repertoire sequencing Rep-seq antibody B cell receptor T cell receptor National Center for Biotechnology Information |
url |
https://www.frontiersin.org/article/10.3389/fimmu.2018.01877/full |
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doaj-e28f95a5137843d3a78e695d29ec81b22020-11-25T00:23:29ZengFrontiers Media S.A.Frontiers in Immunology1664-32242018-08-01910.3389/fimmu.2018.01877402322The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information RepositoriesSyed Ahmad Chan Bukhari0Martin J. O’Connor1Marcos Martínez-Romero2Attila L. Egyedi3Debra Willrett4John Graybeal5Mark A. Musen6Florian Rubelt7Kei-Hoi Cheung8Kei-Hoi Cheung9Kei-Hoi Cheung10Steven H. Kleinstein11Steven H. Kleinstein12Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, United StatesDepartment of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United StatesDepartment of Emergency Medicine, Yale School of Medicine, Yale University, New Haven, CT, United StatesYale Center for Medical Informatics, Yale School of Medicine, Yale University, New Haven, CT, United StatesInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United StatesDepartment of Pathology, Yale School of Medicine, Yale University, New Haven, CT, United StatesInterdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United StatesThe adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses. However, effective sharing of these large-scale data remains a challenge. The AIRR community has proposed minimal information about adaptive immune receptor repertoire (MiAIRR), a standard for reporting AIRR-seq studies. The MiAIRR standard has been operationalized using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientists’ ability to access, find, interoperate, and reuse the data sets. In order to improve metadata quality and ease submission of AIRR-seq studies to the NCBI, we have leveraged the software framework developed by the Center for Expanded Data Annotation and Retrieval (CEDAR), which develops technologies involving the use of data standards and ontologies to improve metadata quality. The resulting CEDAR-AIRR (CAIRR) pipeline enables data submitters to: (i) create web-based templates whose entries are controlled by ontology terms, (ii) generate and validate metadata, and (iii) submit the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive databases. Overall, CAIRR provides a web-based metadata submission interface that supports compliance with the MiAIRR standard. This pipeline is available at http://cairr.miairr.org, and will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies.https://www.frontiersin.org/article/10.3389/fimmu.2018.01877/fullimmune-repertoire sequencingRep-seqantibodyB cell receptorT cell receptorNational Center for Biotechnology Information |