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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018

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1 Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States
2 Beijing Institute of Genomics, Chinese Academy of Sciences., Beijing, China
3 J. Craig Venter Institute, Rockville, Maryland, United States
4 European Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Cambridge, United Kingdom
5 United States Air Force Materiel Command, School of Aerospace Medicine, Wright-Patterson AFB, Ohio, United States
6 DNA Databank of Japan, National Institute of Genetics, Shizuoka, Japan
7 National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
8 N/A, N/A, Bethesda, Maryland, United States
DOI
10.7287/peerj.preprints.3428v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Taxonomy, Virology, Science Policy
Keywords
influenza virus, taxonomy, strain, GenBank, sequence submission
Copyright
© 2017 Hatcher et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Hatcher E, Bao Y, Amedeo P, Blinkova O, Cochrane G, Fedorova N, Gruner W, Leipe D, Nakamura Y, Ostapchuk Y, Palanigobu V, Sanders R, Schoch C, Smith C, Wentworth D, Yankie L, Zhdanov S, Karsch-Mizrachi I, Brister JR. 2017. NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018. PeerJ Preprints 5:e3428v1

Abstract

Currently the National Center of Biotechnology Information (NCBI) assigns individual taxonomy identifiers to each distinct influenza virus isolate submitted to GenBank. To support this practice, individual flu isolates must be manually added to the NCBI taxonomy database and unique taxonomy identifiers generated. This added layer of manual processing is unique to influenza virus and prevents automatization of the flu sequence submission process. Here we outline a new NCBI policy that normalizes influenza virus taxonomy processing but maintains features supported by the previous approach. This change will reduce the amount of manual handling necessary for flu submissions and pave the way for increased automation of the submissions process. While this automation may disrupt some historic practices, it will better align influenza virus data processing with other viruses and ultimately lower the submission burden on data providers.

Author Comment

This is a preprint submission to PeerJ Preprints.

Supplemental Information

Example Source Information table for the programmatic interface

DOI: 10.7287/peerj.preprints.3428v1/supp-1

Example sequence data in FASTA format

DOI: 10.7287/peerj.preprints.3428v1/supp-2

Example Source Information table for the web wizard

DOI: 10.7287/peerj.preprints.3428v1/supp-4

Example Submission Template

DOI: 10.7287/peerj.preprints.3428v1/supp-5

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Eneida Hatcher conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Yiming Bao conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Paolo Amedeo contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Olga Blinkova conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Guy Cochrane reviewed drafts of the paper.

Nadia Fedorova contributed reagents/materials/analysis tools, reviewed drafts of the paper.

William Gruner contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Detlef Leipe conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Yasukazu Nakamura reviewed drafts of the paper.

Yuri Ostapchuk conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Vasuki Palanigobu conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Robert Sanders conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Conrad Schoch conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Catherine Smith contributed reagents/materials/analysis tools, reviewed drafts of the paper.

David Wentworth contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Linda Yankie conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Sergey Zhdanov analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Ilene Karsch-Mizrachi conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

J. Rodney Brister conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The research in this article did not generate any data or code. The data presented in the tables and figures are summaries of publically available data.

Funding

This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine. This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under Award Number U19AI110819. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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NCBI will no longer make taxonomy identifiers for individual influenza strains on January 15, 2018
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