NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium

Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA

Margaret M. and Albert B. Alkek Department of Medicine, Nephrology, Baylor College of Medicine, Houston, TX 77030, USA

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Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA

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School of Medicine, Universidad Central del Caribe, Bayamón, PR 00960, USA

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Genetics & Molecular Biology, Millersville University, 40 Dilworth Rd, Millersville, PA 17551, USA

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Department of Epidemiology of Microbial Diseases, Yale School of Public Health (YSPH), 60 College Street, New Haven, CT 06510, USA

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National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA

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Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA

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AAAS Science and Technology Policy Fellow, Office of Data Science Strategy, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, 31 Center Dr., Bethesda, MD 20894, USA

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MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK

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Biotechnology Graduate Program, University of Maryland Global Campus, 1616 McCormick Drive, Largo, MD 20774, USA

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Boyce Thompson Institute, Ithaca, NY 14850, USA

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School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA

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Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA

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Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA

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School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia

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Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15260, USA

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College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia

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Department of Computer Science, University of Maryland, College Park, MD 20740, USA

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Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20740, USA

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Novel Microdevices, Nucleic Acids, Baltimore, MD 21202, USA

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Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20740, USA

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AgBiome, 104 TW Alexander, Research Triangle, NC 27709, USA

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Bioscience Division, Bikini Atoll Road, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

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Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA

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AAAS Science & Technology Policy Fellow, National Institutes of Health, Center for Information Technology, 6555 Rock Spring Drive, Bethesda, MD 20817, USA

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Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA 90089, USA

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DNANexus, 1975 W El Camino Real #204, Mountain View, CA 94040, USA

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Current affiliation: Department of Biological Sciences, Lehigh University, 111 Research Dr., Bethlehem, PA 18015, USA.

Academic Editors: Manja Marz, Bashar Ibrahim, Franziska Hufsky, Ronald Dijkman, Alban Ramette and Jenna Kelly

Viruses 2020, 12(12), 1424; https://doi.org/10.3390/v12121424

Received: 16 October 2020 / Accepted: 2 December 2020 / Published: 10 December 2020

(This article belongs to the Special Issue Virus Bioinformatics 2020)

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Abstract

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE. View Full-Text

Keywords: data federation; CRISPR; protein domain; metagenomics; virus; genome graphs; HIV-1

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MDPI and ACS Style

Martí-Carreras, J.; Gener, A.R.; Miller, S.D.; Brito, A.F.; Camacho, C.E.; Connor, R.; Deboutte, W.; Glickman, C.; Kristensen, D.M.; Meyer, W.K.; Modha, S.; Norris, A.L.; Saha, S.; Belford, A.K.; Biederstedt, E.; Brister, J.R.; Buchmann, J.P.; Cooley, N.P.; Edwards, R.A.; Javkar, K.; Muchow, M.; Muralidharan, H.S.; Pepe-Ranney, C.; Shah, N.; Shakya, M.; Tisza, M.J.; Tully, B.J.; Vanmechelen, B.; Virta, V.C.; Weissman, J.L.; Zalunin, V.; Efremov, A.; Busby, B. NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index. Viruses 2020, 12, 1424. https://doi.org/10.3390/v12121424

AMA Style

Martí-Carreras J, Gener AR, Miller SD, Brito AF, Camacho CE, Connor R, Deboutte W, Glickman C, Kristensen DM, Meyer WK, Modha S, Norris AL, Saha S, Belford AK, Biederstedt E, Brister JR, Buchmann JP, Cooley NP, Edwards RA, Javkar K, Muchow M, Muralidharan HS, Pepe-Ranney C, Shah N, Shakya M, Tisza MJ, Tully BJ, Vanmechelen B, Virta VC, Weissman JL, Zalunin V, Efremov A, Busby B. NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index. Viruses. 2020; 12(12):1424. https://doi.org/10.3390/v12121424

Chicago/Turabian Style

Martí-Carreras, Joan, Alejandro R. Gener, Sierra D. Miller, Anderson F. Brito, Christiam E. Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, James R. Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara S. Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie C. Virta, Jake L. Weissman, Vadim Zalunin, Alexandre Efremov, and Ben Busby. 2020. "NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index" Viruses 12, no. 12: 1424. https://doi.org/10.3390/v12121424

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