{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T09:49:11Z","timestamp":1785577751947,"version":"3.56.0"},"reference-count":57,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T00:00:00Z","timestamp":1607558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u2013host 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.<\/jats:p>","DOI":"10.3390\/v12121424","type":"journal-article","created":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T20:18:22Z","timestamp":1607631502000},"page":"1424","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["NCBI\u2019s Virus Discovery Codeathon: Building \u201cFIVE\u201d \u2014The Federated Index of Viral Experiments API Index"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0005-9761","authenticated-orcid":false,"given":"Joan","family":"Mart\u00ed-Carreras","sequence":"first","affiliation":[{"name":"Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7875-2358","authenticated-orcid":false,"given":"Alejandro","family":"Gener","sequence":"additional","affiliation":[{"name":"Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"Margaret M. and Albert B. Alkek Department of Medicine, Nephrology, Baylor College of Medicine, Houston, TX 77030, USA"},{"name":"Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA"},{"name":"School of Medicine, Universidad Central del Caribe, Bayam\u00f3n, PR 00960, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3200-428X","authenticated-orcid":false,"given":"Sierra","family":"Miller","sequence":"additional","affiliation":[{"name":"Genetics &amp; Molecular Biology, Millersville University, 40 Dilworth Rd, Millersville, PA 17551, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5785-7222","authenticated-orcid":false,"given":"Anderson","family":"Brito","sequence":"additional","affiliation":[{"name":"Department of Epidemiology of Microbial Diseases, Yale School of Public Health (YSPH), 60 College Street, New Haven, CT 06510, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6709-8298","authenticated-orcid":false,"given":"Christiam","family":"Camacho","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Connor","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3829-1056","authenticated-orcid":false,"given":"Ward","family":"Deboutte","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6648-4832","authenticated-orcid":false,"given":"Cody","family":"Glickman","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Kristensen","sequence":"additional","affiliation":[{"name":"Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7978-3877","authenticated-orcid":false,"given":"Wynn","family":"Meyer","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8440-885X","authenticated-orcid":false,"given":"Sejal","family":"Modha","sequence":"additional","affiliation":[{"name":"MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0442-9096","authenticated-orcid":false,"given":"Alexis","family":"Norris","sequence":"additional","affiliation":[{"name":"Biotechnology Graduate Program, University of Maryland Global Campus, 1616 McCormick Drive, Largo, MD 20774, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1160-1413","authenticated-orcid":false,"given":"Surya","family":"Saha","sequence":"additional","affiliation":[{"name":"Boyce Thompson Institute, Ithaca, NY 14850, USA"},{"name":"School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1912-4201","authenticated-orcid":false,"given":"Anna","family":"Belford","sequence":"additional","affiliation":[{"name":"Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evan","family":"Biederstedt","sequence":"additional","affiliation":[{"name":"Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Brister","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6842-1229","authenticated-orcid":false,"given":"Jan","family":"Buchmann","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6029-304X","authenticated-orcid":false,"given":"Nicholas","family":"Cooley","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15260, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8383-8949","authenticated-orcid":false,"given":"Robert","family":"Edwards","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1638-6625","authenticated-orcid":false,"given":"Kiran","family":"Javkar","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland, College Park, MD 20740, USA"},{"name":"Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20740, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2825-4120","authenticated-orcid":false,"given":"Michael","family":"Muchow","sequence":"additional","affiliation":[{"name":"Novel Microdevices, Nucleic Acids, Baltimore, MD 21202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harihara","family":"Muralidharan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland, College Park, MD 20740, USA"},{"name":"Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20740, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Pepe-Ranney","sequence":"additional","affiliation":[{"name":"AgBiome, 104 TW Alexander, Research Triangle, NC 27709, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nidhi","family":"Shah","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland, College Park, MD 20740, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Migun","family":"Shakya","sequence":"additional","affiliation":[{"name":"Bioscience Division, Bikini Atoll Road, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Tisza","sequence":"additional","affiliation":[{"name":"Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9384-7635","authenticated-orcid":false,"given":"Benjamin","family":"Tully","sequence":"additional","affiliation":[{"name":"Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8350-4356","authenticated-orcid":false,"given":"Bert","family":"Vanmechelen","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Virta","sequence":"additional","affiliation":[{"name":"AAAS Science &amp; Technology Policy Fellow, National Institutes of Health, Center for Information Technology, 6555 Rock Spring Drive, Bethesda, MD 20817, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4237-4807","authenticated-orcid":false,"given":"JL","family":"Weissman","sequence":"additional","affiliation":[{"name":"Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7722-1958","authenticated-orcid":false,"given":"Vadim","family":"Zalunin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Efremov","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5267-4988","authenticated-orcid":false,"given":"Ben","family":"Busby","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA"},{"name":"DNANexus, 1975 W El Camino Real #204, Mountain View, CA 94040, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature09796","article-title":"A decade\u2019s perspective on DNA sequencing technology","volume":"470","author":"Mardis","year":"2011","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The sequence read archive: Explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_3","unstructured":"(2020, December 03). SRA Database Growth, Available online: https:\/\/www.ncbi.nlm.nih.gov\/sra\/docs\/sragrowth\/."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Connor, R., Brister, R., Buchmann, J., Deboutte, W., Edwards, R., Mart\u00ed-Carreras, J., Tisza, M., Zalunin, V., Andrade-Mart\u00ednez, J., and Cantu, A. (2019). NCBI\u2019s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes (Basel)., 10.","DOI":"10.3390\/genes10090714"},{"key":"ref_5","unstructured":"(2020, December 03). STRIDES Initiative, Available online: https:\/\/datascience.nih.gov\/strides."},{"key":"ref_6","unstructured":"(2020, December 03). NIH Strategic Plan for Data Science, Available online: https:\/\/datascience.nih.gov\/strategicplan."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"D23","DOI":"10.1093\/nar\/gky1069","article-title":"Database resources of the National Center for Biotechnology Information","volume":"47","author":"Sayers","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_8","unstructured":"(2020, December 03). NCBI Codeathons. Available online: https:\/\/ncbi-codeathons.github.io\/."},{"key":"ref_9","unstructured":"Busby, B., Saha, S., and Mart\u00ed-Carreras, J. (2019, December 04). Virus Discovery Project 2019. Available online: https:\/\/osf.io\/g9w8r\/."},{"key":"ref_10","unstructured":"(2020, December 03). NCBI-Codeathons\/Virus_Graphs. Available online: https:\/\/github.com\/NCBI-Codeathons\/Virus_Graphs\/tree\/master\/data."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1101\/gr.214155.116","article-title":"Genome graphs and the evolution of genome inference","volume":"27","author":"Paten","year":"2017","journal-title":"Genome Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"D593","DOI":"10.1093\/nar\/gkr859","article-title":"ViPR: An Open Bioinformatics Database and Analysis Resource for Virology Research","volume":"40","author":"Pickett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_13","unstructured":"(2020, December 03). NCBI-Hackathons\/VirusDiscoveryProject. Available online: https:\/\/github.com\/NCBI-Hackathons\/VirusDiscoveryProject."},{"key":"ref_14","unstructured":"(2020, December 03). NCBI-Codeathons\/Domain_HMM_Boundaries. Available online: https:\/\/github.com\/NCBI-Codeathons\/Domain_HMM_Boundaries\/tree\/master\/viral-cdd-models."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST plus: Architecture and applications. BMC Bioinformatics, 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: Fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"ref_17","unstructured":"(2020, December 03). NCBI-Codeathons\/Domain_HMM_Boundaries. Available online: https:\/\/github.com\/NCBI-Codeathons\/Domain_HMM_Boundaries\/blob\/master\/dataset_accessions\/Mash_accessions.txt."},{"key":"ref_18","unstructured":"(2020, December 10). R Core Team R: A Language and Environment for Statistical Computing 2019. Available online: https:\/\/www.r-project.org\/."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Bougeard, S., and Dray, S. (2018). Supervised Multiblock Analysis in R with the ade4 Package. J. Stat. Softw., 86.","DOI":"10.18637\/jss.v086.i01"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: Phylogenetic analysis in R","volume":"27","author":"Schliep","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1093\/bioinformatics\/btv428","article-title":"dendextend: An R package for visualizing, adjusting and comparing trees of hierarchical clustering","volume":"31","author":"Galili","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Eddy, S.R. (2011). Accelerated profile HMM searches. PLoS Comput. Biol., 7.","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation","volume":"44","author":"Wright","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_24","unstructured":"(2020, December 03). Domain_HMM_Boundaries\/viral-cdd-models\/virus_models.txt. Available online: https:\/\/github.com\/NCBI-Codeathons\/Domain_HMM_Boundaries\/blob\/master\/viral-cdd-models\/virus_models.txt."},{"key":"ref_25","unstructured":"(2020, December 03). Conserved Domains and Protein Classification Help, Available online: https:\/\/www.ncbi.nlm.nih.gov\/Structure\/cdd\/cdd_help.shtml."},{"key":"ref_26","unstructured":"(2020, December 03). Domain_HMM_Boundaries\/scripts\/tReads.py. Available online: https:\/\/github.com\/NCBI-Codeathons\/Domain_HMM_Boundaries\/tree\/master\/scripts\/tReads.py."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"D482","DOI":"10.1093\/nar\/gkw1065","article-title":"Virus Variation Resource\u2014Improved response to emergent viral outbreaks","volume":"45","author":"Hatcher","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1093\/bioinformatics\/btw711","article-title":"PhagesDB: The actinobacteriophage database","volume":"33","author":"Russell","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkn741","article-title":"Database resources of the National Center for Biotechnology Information","volume":"37","author":"Sayers","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_30","unstructured":"(2020, December 03). NCBI-Codeathons\/Host_Phage_Interactions. Available online: https:\/\/github.com\/NCBI-Codeathons\/Host_Phage_Interactions\/tree\/development\/src."},{"key":"ref_31","unstructured":"(2020, December 03). CRISPR-Cas++. Available online: https:\/\/crisprcas.i2bc.paris-saclay.fr\/Home\/Download."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1089\/crispr.2018.0034","article-title":"Selective Maintenance of Multiple CRISPR Arrays Across Prokaryotes","volume":"1","author":"Weissman","year":"2018","journal-title":"Cris. J."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Biswas, A., Staals, R.H.J., Morales, S.E., Fineran, P.C., and Brown, C.M. (2016). CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genom., 17.","DOI":"10.1186\/s12864-016-2627-0"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41586-019-1058-x","article-title":"New insights from uncultivated genomes of the global human gut microbiome","volume":"568","author":"Nayfach","year":"2019","journal-title":"Nature"},{"key":"ref_36","unstructured":"(2020, December 03). ctSkennerton\/minced. Available online: https:\/\/github.com\/ctSkennerton\/minced."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C., and Hugenholtz, P. (2007). CRISPR Recognition Tool (CRT): A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-209"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Parks, D.H., Chuvochina, M., Chaumeil, P.A., Rinke, C., Mussig, A.J., and Hugenholtz, P. (2019). Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy. bioRxiv, 771964.","DOI":"10.1101\/771964"},{"key":"ref_39","unstructured":"(2020, December 03). NCBI-Codeathons\/Virus_Graphs. Available online: https:\/\/github.com\/NCBI-Codeathons\/Virus_Graphs."},{"key":"ref_40","unstructured":"(2020, December 03). Virus_Graphs\/Reference_Seq.fasta. Available online: https:\/\/github.com\/NCBI-Codeathons\/Virus_Graphs\/blob\/master\/Reference_Seq.fasta."},{"key":"ref_41","unstructured":"(2020, December 03). HIV Databases, Available online: http:\/\/www.hiv.lanl.gov\/."},{"key":"ref_42","unstructured":"(2020, December 03). HIV Sequence Database, Available online: https:\/\/www.hiv.lanl.gov\/content\/sequence\/HIV\/mainpage.html."},{"key":"ref_43","unstructured":"Varoquaux, G., Vaught, T., and Millman, J. (2008, January 19\u201324). Exploring Network Structure, Dynamics, and Function using NetworkX. Proceedings of the 7th Python in Science Conference, Pasadena, CA, USA."},{"key":"ref_44","unstructured":"(2020, December 03). NCBI-Codeathons\/The_Virus_Index. Available online: https:\/\/github.com\/NCBI-Codeathons\/The_Virus_Index\/tree\/master\/python."},{"key":"ref_45","unstructured":"(2020, December 03). The_Virus_Index\/schema. Available online: https:\/\/github.com\/NCBI-Codeathons\/The_Virus_Index\/tree\/master\/schema."},{"key":"ref_46","unstructured":"(2020, December 03). viral-index 0.0.3. Available online: https:\/\/test.pypi.org\/project\/viral-index\/."},{"key":"ref_47","unstructured":"(2020, December 03). NCBI-Codeathons\/The_Virus_Index. Available online: https:\/\/github.com\/NCBI-Codeathons\/The_Virus_Index."},{"key":"ref_48","unstructured":"(2020, December 03). Viral-index API. Available online: https:\/\/github.com\/NCBI-Codeathons\/The_Virus_Index#api."},{"key":"ref_49","unstructured":"Broder, A.Z. (1997, January 13). On the Resemblance and Containment of Documents. Proceedings of the Compression and Complexity of SEQUENCES 1997 (Cat. No.97TB100171), Washington, DC, USA."},{"key":"ref_50","unstructured":"(2020, December 03). Domain_HMM_Boundaries\/dataset_accessions\/RPStbln_accessions.txt. Available online: https:\/\/github.com\/NCBI-Codeathons\/Domain_HMM_Boundaries\/blob\/master\/dataset_accessions\/RPStbln_accessions.txt."},{"key":"ref_51","unstructured":"(2020, December 03). The Open Graph Viz Platform. Available online: https:\/\/gephi.org."},{"key":"ref_52","unstructured":"(2020, December 03). Cytoscape. Available online: https:\/\/cytoscape.org\/."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_54","unstructured":"(2020, December 03). Google Cloud Platform. Available online: https:\/\/console.cloud.google.com\/bigquery?p=virus-hunting-2-codeathon&d=viasq&page=dataset."},{"key":"ref_55","unstructured":"(2020, December 03). Sample Code. Available online: https:\/\/github.com\/NCBI-Codeathons\/The_Virus_Index#sample-code."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"D583","DOI":"10.1093\/nar\/gku1121","article-title":"VirHostNet 2.0: Surfing on the web of virus\/host molecular interactions data","volume":"43","author":"Guirimand","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/12\/1424\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:43:36Z","timestamp":1760179416000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/12\/1424"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,10]]},"references-count":57,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,12]]}},"alternative-id":["v12121424"],"URL":"https:\/\/doi.org\/10.3390\/v12121424","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,10]]}}}