{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T10:07:41Z","timestamp":1767262061488,"version":"3.37.3"},"reference-count":126,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T00:00:00Z","timestamp":1705536000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000092","name":"U.S. National Library of Medicine","doi-asserted-by":"publisher","award":["T5 Biomedical Informatics and Data Science Research Training Programs"],"award-info":[{"award-number":["T5 Biomedical Informatics and Data Science Research Training Programs"]}],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000092","name":"U.S. National Library of Medicine","doi-asserted-by":"publisher","award":["T5 Biomedical Informatics and Data Science Research Training Programs"],"award-info":[{"award-number":["T5 Biomedical Informatics and Data Science Research Training Programs"]}],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NIH","award":["NCATS 1UL1TR001412 (Buffalo Clinical and Translational Research Center)"],"award-info":[{"award-number":["NCATS 1UL1TR001412 (Buffalo Clinical and Translational Research Center)"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies\u2013structured, controlled, vocabularies\u2013are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.<\/jats:p>","DOI":"10.1371\/journal.pone.0285093","type":"journal-article","created":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T18:35:13Z","timestamp":1705602913000},"page":"e0285093","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Coordinating virus research: The Virus Infectious Disease Ontology"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1118-1738","authenticated-orcid":true,"given":"John","family":"Beverley","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shane","family":"Babcock","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gustavo","family":"Carvalho","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lindsay G.","family":"Cowell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Duesing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Regina","family":"Hurley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Merrell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard H.","family":"Scheuermann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry","family":"Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,1,18]]},"reference":[{"key":"pone.0285093.ref001","article-title":"The Pivotal Role of TMPRSS2 in Coronavirus Disease 2019 and Prostate Cancer","author":"V Mollica","year":"2020","journal-title":"Future Oncology"},{"key":"pone.0285093.ref002","article-title":"TMPRSS2 and COVID-19: Serendipity or Opportunity for Intervention?","author":"K Stopsack","year":"2020","journal-title":"Cancer Discovery"},{"issue":"9","key":"pone.0285093.ref003","doi-asserted-by":"crossref","DOI":"10.1016\/j.jaccas.2020.04.027","article-title":"Sex Differences in Mortality from COVID-19 Pandemic","volume":"2","author":"G Sharma","year":"2020","journal-title":"JACC Case Reports"},{"key":"pone.0285093.ref004","article-title":"Gender Differences in Patients with COVID-19: Focus on Severity and Mortality","author":"J Jin","year":"2020","journal-title":"Frontiers in Public Health"},{"issue":"1581","key":"pone.0285093.ref005","article-title":"COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning","volume":"11","author":"E Ong","year":"2020","journal-title":"Front. Immunol"},{"issue":"16","key":"pone.0285093.ref006","article-title":"Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection","volume":"8","author":"Y Liu","year":"2021","journal-title":"Scientific Data"},{"key":"pone.0285093.ref007","doi-asserted-by":"crossref","first-page":"D693","DOI":"10.1093\/nar\/gky999","article-title":"Victors: a web-based knowledge base of virulence factors in human and animal pathogens","volume":"47","author":"S Sayers","year":"2019","journal-title":"Nucleic Acid Res"},{"key":"pone.0285093.ref008","article-title":"Epidemiological Characteristics of 2143 Pediatric Patients with 2019 Coronavirus Disease in China","author":"Y Dong","year":"2020","journal-title":"Pediatrics"},{"issue":"23","key":"pone.0285093.ref009","doi-asserted-by":"crossref","first-page":"2427","DOI":"10.1001\/jama.2020.8707","article-title":"Nasal Gene Expression of Angiotensin-Converting Enzyme 2 in Children and Adults","volume":"323","author":"S. Bunyavanich","year":"2020","journal-title":"JAMA"},{"volume-title":"Building Ontologies with Basic Formal Ontology","year":"2015","author":"MA: MIT Press","key":"pone.0285093.ref010"},{"issue":"7","key":"pone.0285093.ref011","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41597-020-0523-6","article-title":"CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis","author":"Y He","year":"2020","journal-title":"Scientific data"},{"key":"pone.0285093.ref012","article-title":"Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package","author":"EJ Griffiths","year":"2022","journal-title":"Gigascience"},{"issue":"8","key":"pone.0285093.ref013","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1038\/nbt.1411","article-title":"Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project","volume":"26","author":"CF Taylor","year":"2008","journal-title":"Nat Biotechnol"},{"issue":"4","key":"pone.0285093.ref014","doi-asserted-by":"crossref","first-page":"e0154556","DOI":"10.1371\/journal.pone.0154556","article-title":"The Ontology for Biomedical Investigations","volume":"11","author":"A Bandrowski","year":"2016","journal-title":"PLoS ONE"},{"key":"pone.0285093.ref015","first-page":"373","volume-title":"Infectious Disease Informatics","author":"Infectious Diseases Ontology","year":"2010"},{"issue":"1","key":"pone.0285093.ref016","doi-asserted-by":"crossref","DOI":"10.1186\/s13326-021-00245-1","article-title":"The Infectious Disease Ontology in the age of COVID-19","volume":"12","author":"S Babcock","year":"2021","journal-title":"J Biomed Semantics"},{"key":"pone.0285093.ref017","first-page":"1223","article-title":"BioPortal: Ontologies and Data Resources with the Click of a Mouse","author":"M Musen","year":"2008","journal-title":"AMIA Annu Symp Proc"},{"key":"pone.0285093.ref018","unstructured":"The Open Biomedical Ontologies Foundry. http:\/\/obofoundry.org\/ Accessed 11 Mar 2023."},{"key":"pone.0285093.ref019","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt1346","article-title":"The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration","volume":"25","author":"B Smith","year":"2007","journal-title":"Nat Biotechnol"},{"volume-title":"An Introduction to Description Logic","year":"2017","author":"University Press","key":"pone.0285093.ref020"},{"key":"pone.0285093.ref021","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4614-0682-2","volume-title":"Computability and Complexity Theory: Texts in Computer Science","author":"H Homer","year":"2011","edition":"2"},{"key":"pone.0285093.ref022","article-title":"HermiT: A Highly-Efficient OWL Reasoner","author":"R Shearer","year":"2008","journal-title":"OWLED"},{"issue":"2","key":"pone.0285093.ref023","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.websem.2007.03.004","volume":"5","author":"BP Evren Sirin","year":"2007","journal-title":"Pellet: A practical OWL-DL reasoner Web Semantics: Science, Services and Agents on the World Wide Web"},{"key":"pone.0285093.ref024","doi-asserted-by":"crossref","first-page":"D330","DOI":"10.1093\/nar\/gky1055","article-title":"The Gene Ontology Resource: 20 years and still GOing","volume":"47","author":"The Gene Ontology Consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pone.0285093.ref025","first-page":"25","article-title":"The Gene Ontology Consortium","volume":"25","author":"Gene ontology: tool for the unification of biology","year":"2000","journal-title":"Nature genetics"},{"issue":"4","key":"pone.0285093.ref026","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1111\/j.1467-9329.2012.00557.x","article-title":"Classifying Processes: An Essay in Applied Ontology","author":"B. Smith","year":"2012","journal-title":"Ratio"},{"key":"pone.0285093.ref027","unstructured":"Smith B. (2012) On Classifying Material Entities in Basic Formal Ontology. Interdisciplinary Ontology: Proceedings of the Third Interdisciplinary Ontology Meeting. Tokyo: Keio University Press. 1\u201313."},{"issue":"11","key":"pone.0285093.ref028","doi-asserted-by":"crossref","first-page":"103","DOI":"10.3233\/AO-160164","article-title":"Functions in Basic Formal Ontology","author":"A Spear","year":"2016","journal-title":"Applied Ontology"},{"key":"pone.0285093.ref029","first-page":"17","article-title":"Basic Formal Ontology","author":"BFO","year":"2022","journal-title":"Applied Ontology"},{"key":"pone.0285093.ref030","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/1471-2105-10-125","article-title":"Survey-based naming conventions for use in OBO Foundry ontology development","volume":"10","author":"D Schober","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"pone.0285093.ref031","first-page":"175","article-title":"Definitions in Ontologies","volume":"109","author":"S Seppala","year":"2016","journal-title":"Cahiers de Lexicologie"},{"key":"pone.0285093.ref032","unstructured":"Goldfain A, Smith B, Cowell LG. (2010) Dispositions and the infectious disease ontology. In: Galton A, Mizoguchi R, editors. Formal Ontology in Information Systems: Proceedings of the 6th International Conference (FOIS 2010). Amsterdam: IOS Press."},{"key":"pone.0285093.ref033","article-title":"Introduction: Ontologies, Semantic Technologies, and Intelligence","author":"T. Janssen","year":"2010","journal-title":"Ontologies and Semantic Technologies for Intelligence"},{"key":"pone.0285093.ref034","article-title":"Brucellosis ontology (IDOBRU) as an extension of the infectious disease ontology","author":"Y Lin","year":"2011","journal-title":"J Biomed Semant"},{"key":"pone.0285093.ref035","article-title":"Ontology-based representation and analysis of host-Brucella interactions","author":"Y Lin","year":"2015","journal-title":"J Biomed Semant"},{"key":"pone.0285093.ref036","article-title":"The Influenza Infectious Disease Ontology (I-IDO)","author":"J Luciano","year":"2008","journal-title":"The 11th Annual Bio-Ontologies Meeting, ISMB"},{"issue":"1","key":"pone.0285093.ref037","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13326-022-00279-z","article-title":"A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology","volume":"13","author":"Y He","year":"2022","journal-title":"J Biomed Semantics"},{"key":"pone.0285093.ref038","first-page":"116","article-title":"Towards an Ontological Treatment of Disease and Diagnosis","author":"R Scheuermann","year":"2009","journal-title":"AMIA Joint Summit on Translational Science"},{"key":"pone.0285093.ref039","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/s12866-015-0481-x","article-title":"Representing Virus-Host Interactions and other Multi-Organism Processes in the Gene Ontology","volume":"15","author":"RE Foulger","year":"2015","journal-title":"BMC Microbiology"},{"key":"pone.0285093.ref040","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1371\/journal.pone.0171746","article-title":"The Ins and Outs of Eukaryotic Viruses: Knowledge Base and Ontology of a Viral Infection","volume":"12","author":"C Hulo","year":"2017","journal-title":"PLoS One"},{"key":"pone.0285093.ref041","article-title":"How the Virophage Compels the Need to Readdress the Classification of Microbes","author":"D. Raoult","year":"2014","journal-title":"Virology"},{"key":"pone.0285093.ref042","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nrmicro1858","article-title":"Redefining Viruses: Lessons from Mimivirus","volume":"6","author":"D. Roault","year":"2008","journal-title":"Nature Reviews Microbiology"},{"key":"pone.0285093.ref043","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.shpsc.2016.02.016","article-title":"Are Viruses Alive? The Replicator Paradigm Sheds Decisive Light on an Old but Misguided Question","volume":"59","author":"EV Koonin","year":"2016","journal-title":"Studies in History and Philosophy of Science"},{"key":"pone.0285093.ref044","unstructured":"Claverie JM. (2008) Encyclopedia of Virology 3rd Edition."},{"key":"pone.0285093.ref045","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/s00705-015-2622-9","article-title":"A Classification System for Virophages and Satellite Viruses","volume":"161","author":"M Krupovic","year":"2016","journal-title":"Archives of Virology"},{"key":"pone.0285093.ref046","article-title":"Giant Viruses and Their Virophage Parasites","author":"AL Rodrigo","year":"2019","journal-title":"Reference Module in Life Sciences"},{"key":"pone.0285093.ref047","doi-asserted-by":"crossref","unstructured":"He Y. (2022). Ontological Classification of Self-replicating Organic Structures. Preprint. 1\u20138. doi: 10.31219\/osf.io\/n2zkh","DOI":"10.31219\/osf.io\/n2zkh"},{"key":"pone.0285093.ref048","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI Taxonomy Database","volume":"40","author":"S. Federhen","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pone.0285093.ref049","article-title":"A Comprehensive and Quantitative Exploration of Thousands of Viral Genomes","author":"G Mahmoudabadi","year":"2018","journal-title":"eLife"},{"key":"pone.0285093.ref050","article-title":"Virus Taxonomy","author":"J. Kuhn","year":"2020","journal-title":"Reference Modules in Life Sciences"},{"key":"pone.0285093.ref051","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1756-0500-3-175","article-title":"OntoFox: webbased support for ontology reuse","volume":"3","author":"Z Xiang","year":"2010","journal-title":"BMC research notes"},{"key":"pone.0285093.ref052","unstructured":"Dimmock NJ, et. al. (2007). Introduction to Modern Virology. 6th edition. Blackwell Publishing."},{"journal-title":"Principles of Molecular Virology","year":"2016","author":"Academic Press","key":"pone.0285093.ref053"},{"key":"pone.0285093.ref054","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1128\/br.35.3.235-241.1971","article-title":"Expression of Animal Virus Genomes","volume":"35","author":"D. Baltimore","year":"1971","journal-title":"Bacteriological Reviews"},{"key":"pone.0285093.ref055","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-2438-7_1","article-title":"Coronavirus: An Overview of their Replication and Pathogenesis","volume":"1282","author":"H Maier","year":"2015","journal-title":"Coronaviruses"},{"volume-title":"Microbiology with Disease Taxonomy","year":"2017","author":"R. Bauman","key":"pone.0285093.ref056"},{"issue":"6","key":"pone.0285093.ref057","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/gb-2006-7-6-110","article-title":"Viruses take Center Stage in Cellular Evolution","volume":"7","author":"J. Claverie","year":"2006","journal-title":"Genome Biology"},{"issue":"2","key":"pone.0285093.ref058","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/s11084-010-9194-1","article-title":"Defining Life: The Virus Viewpoint","volume":"40","author":"P. Forterre","year":"2010","journal-title":"Origins of Life Evolution Biosphere"},{"issue":"12","key":"pone.0285093.ref059","doi-asserted-by":"crossref","first-page":"6895","DOI":"10.1073\/pnas.111085598","article-title":"RNA Virus Error Catastrophe: Direct Molecular Test by Using Ribavarin","volume":"98","author":"S. Crotty","year":"2001","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"12","key":"pone.0285093.ref060","doi-asserted-by":"crossref","first-page":"7289","DOI":"10.1073\/pnas.1232294100","article-title":"A Single Mutation in Poliovirus RNA-Dependent RNA Polymerase Confers Resistance to Mutagenic Nucleotide Analogs via Increased Fidelity","volume":"100","author":"J. Pfeiffer","year":"2003","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pone.0285093.ref061","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkm791","article-title":"ChEBI: a database and ontology for chemical entities of biological interest","volume":"36","author":"K Degtyarenko","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"pone.0285093.ref062","doi-asserted-by":"crossref","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: Improved services and an expanding collection of metabolites","volume":"44","author":"J. Hastings","year":"2016","journal-title":"Nucleic acids research"},{"issue":"26","key":"pone.0285093.ref063","doi-asserted-by":"crossref","first-page":"10771","DOI":"10.1073\/pnas.1305923110","article-title":"Bacteriophage Adhering to Mucus Provide a Non-Host Derived Immunity","volume":"110","author":"JJ Barr","year":"2013","journal-title":"PNAS"},{"issue":"23","key":"pone.0285093.ref064","doi-asserted-by":"crossref","first-page":"10475","DOI":"10.1073\/pnas.1307782110","article-title":"Sticky Bacteriophage Protect Animal Cells","volume":"110","author":"JR Meyer","year":"2013","journal-title":"PNAS"},{"key":"pone.0285093.ref065","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1105\/tpc.16.00931","article-title":"Mechanisms to mitigate the trade-off between growth and defense","volume":"29","author":"TL Karasov","year":"2017","journal-title":"Plant Cell"},{"key":"pone.0285093.ref066","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aad0917","article-title":"Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability","volume":"8","author":"M Yassour","year":"2016","journal-title":"Sci. Transl. Med"},{"key":"pone.0285093.ref067","first-page":"20143085","article-title":"Evolution of the immune system in humans from infancy to old age","volume":"282","author":"AK Simon","year":"2015","journal-title":"Proc. R. Soc. Lond"},{"issue":"1783","key":"pone.0285093.ref068","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2019.0066","article-title":"The legacy of larval infection on immunological dynamics over metamorphosis","volume":"374","author":"JT Critchlow","year":"2019","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"pone.0285093.ref069","volume-title":"Textbook of Microbiology","author":"R. Ananthanarayan","year":"2005","edition":"7"},{"issue":"6593","key":"pone.0285093.ref070","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/382722a0","article-title":"Resistance to HIV-1 Infection in Caucasian Individuals bearing Mutant Alleles of the CCR-5 Chemokine Receptor Gene","volume":"382","author":"M. Samson","year":"1996","journal-title":"Nature"},{"issue":"12","key":"pone.0285093.ref071","doi-asserted-by":"crossref","first-page":"4853","DOI":"10.1182\/blood-2004-12-4948","article-title":"The hydration state of human red blood cells and their susceptibility invasion by Plasmodium falciparum","volume":"105","author":"T Tiffert","year":"2005","journal-title":"Blood"},{"key":"pone.0285093.ref072","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.jbi.2010.02.008","article-title":"Towards an ontological representation of resistance: the case of MRSA","volume":"44","author":"A Goldfain","year":"2011","journal-title":"J Biomed Inform"},{"key":"pone.0285093.ref073","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1098\/rstb.2004.1489","article-title":"The aetiology of SARS: Koch\u2019s postulates fulfilled","volume":"359","author":"AD Osterhaus","year":"2004","journal-title":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences"},{"issue":"2","key":"pone.0285093.ref074","doi-asserted-by":"crossref","first-page":"S274","DOI":"10.1093\/cid\/10.Supplement_2.S274","article-title":"Molecular Koch\u2019s postulates applied to microbial pathogenicity","volume":"10","author":"S. Falkow","year":"1988","journal-title":"Rev Infect Dis"},{"key":"pone.0285093.ref075","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/jb.33.1.1-12.1937","article-title":"Viruses and Koch\u2019s Postulates","volume":"33","author":"TM Rivers","year":"1937","journal-title":"Journal of bacteriology"},{"key":"pone.0285093.ref076","first-page":"136","article-title":"Common themes in microbial pathogenicity revisited","volume":"61","author":"BB Finlay","year":"1997","journal-title":"Microbiol. Mol. Biol. Rev"},{"key":"pone.0285093.ref077","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1046\/j.1365-2958.1997.3101672.x","article-title":"Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution","volume":"23","author":"J Hacker","year":"1997","journal-title":"Mol. Microbiol"},{"key":"pone.0285093.ref078","doi-asserted-by":"crossref","unstructured":"Yu H, et al. (2022) A New Framework for Host-Pathogen Interaction Research. Frontiers in Immunology. doi: 10.3389\/fimmu.2022.1066733","DOI":"10.3389\/fimmu.2022.1066733"},{"issue":"4","key":"pone.0285093.ref079","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.01175-20","article-title":"Pathogenesis of COVID-19 from the Perspective of the Damage-Response Framework","volume":"11","author":"L Pirofski","year":"2020","journal-title":"MBio"},{"issue":"8","key":"pone.0285093.ref080","doi-asserted-by":"crossref","first-page":"775","DOI":"10.4161\/21505594.2014.960726","article-title":"What is a Pathogen? Towards a Process View of Host-Parasite Interactions","volume":"5","author":"P Methot","year":"2014","journal-title":"Virulence"},{"key":"pone.0285093.ref081","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/nrmicro732","article-title":"The Damage-Response Framework of Microbial Pathogenesis","volume":"1","author":"A Casadevall","year":"2003","journal-title":"Nature Reviews Microbiology"},{"key":"pone.0285093.ref082","article-title":"Pathogenesis of COVID-19 from the Perspective of the Damage-Response Framework","author":"T Morrison","year":"2020","journal-title":"Host-Microbe Biology"},{"key":"pone.0285093.ref083","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.2147\/JMDH.S357867","article-title":"Association Between Symptoms and Severity of Disease in Hospitalised Novel Coronavirus (COVID-19) Patients: A Systematic Review and Meta-Analysis","volume":"15","author":"A Talukder","year":"2022","journal-title":"J Multidiscip Healthc"},{"key":"pone.0285093.ref084","unstructured":"Centers for Disease Control and Prevention. (2020). Coronavirus Disease 2019 (COVID-19) 2020 Interim Case Definition, Approved April 2, 2020. https:\/\/ndc.services.cdc.gov\/case-definitions\/coronavirus-disease-2019-2020\/ Accessed Mar 11 2023."},{"key":"pone.0285093.ref085","unstructured":"Council of State of Territorial Epidemiologists. (2023). Standardization Surveillance Case Definition and National Notification for 2019 Coronavirus Disease (COVID-19). https:\/\/ndc.services.cdc.gov\/conditions\/coronavirus-disease-2019-covid-19\/ Accessed Mar 11 2023."},{"key":"pone.0285093.ref086","unstructured":"Centers for Disease Control and Prevention. (2023). Coronavirus Disease 2019 (COVID-19) 2023 Case Definition, Approved February 28, 2023. https:\/\/ndc.services.cdc.gov\/case-definitions\/coronavirus-disease-2019-covid-19\/ Accessed Mar 11 2023."},{"issue":"4","key":"pone.0285093.ref087","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1289\/ehp.1002383","article-title":"Global influenza seasonality: reconciling patterns across temperate and tropical regions","volume":"119","author":"J Tamerius","year":"2011","journal-title":"Environ Health Perspect"},{"issue":"14","key":"pone.0285093.ref088","article-title":"Network-based Drug Repurposing for Novel Coronavirus 2019-nCoV\/SARS-CoV-2","volume":"6","author":"Y. Zhou","year":"2020","journal-title":"Cell Discovery"},{"issue":"1","key":"pone.0285093.ref089","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1146\/annurev-virology-110615-042301","article-title":"Structure, Function, and Evolution of Coronavirus Spike Proteins","volume":"3","author":"F. Li","year":"2016","journal-title":"Annu Rev Virol"},{"key":"pone.0285093.ref090","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s12985-019-1182-0","article-title":"Coronavirus envelope protein: current knowledge","volume":"16","author":"D Schoeman","year":"2019","journal-title":"Virol J"},{"key":"pone.0285093.ref091","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1159\/000503030","article-title":"Innate Immune Evasion by Human Respiratory RNA Viruses","volume":"12","author":"M. Kikkert","year":"2020","journal-title":"J Innate Immun"},{"key":"pone.0285093.ref092","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/s41577-020-0311-8","article-title":"The trinity of COVID-19: immunity, inflammation and intervention","volume":"20","author":"MZ Tay","year":"2020","journal-title":"Nat Rev Immunol"},{"key":"pone.0285093.ref093","article-title":"Ontology-based Systematic Classification and Analysis of Coronaviruses, Hosts, and Host-Coronavirus Interactions towards Deep Understanding of COVID-19","author":"H Yu","year":"2020","journal-title":"arXiv preprint"},{"key":"pone.0285093.ref094","first-page":"1","article-title":"Comparison of coronavirus disease 2019 (COVID-19) symptoms at diagnosis among healthcare personnel before and after the emergence of the omicron variant","author":"J Laracy","year":"2022","journal-title":"Infection Control & Hospital Epidemiology"},{"issue":"1","key":"pone.0285093.ref095","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s40779-020-00240-0","article-title":"The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak\u2013an update on the status","volume":"7","author":"YR Guo","year":"2020","journal-title":"Military Medical Research"},{"issue":"3","key":"pone.0285093.ref096","first-page":"e7343","article-title":"Acetazolamide, Nifedipine and Phosphodiesterase Inhibitors: Rationale for Their Utilization as Adjunctive Countermeasures in the Treatment of Coronavirus Disease 2019 (COVID-19)","volume":"12","author":"I Solaimanzadeh","year":"2020","journal-title":"Cureus"},{"key":"pone.0285093.ref097","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/nm1267","article-title":"A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury","volume":"11","author":"K Kuba","year":"2005","journal-title":"Nature medicine"},{"key":"pone.0285093.ref098","article-title":"Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses","author":"M Letko","year":"2020","journal-title":"Nature microbiology"},{"key":"pone.0285093.ref099","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1002\/jmv.25681","article-title":"Emerging coronaviruses: Genome structure, replication, and pathogenesis","volume":"92","author":"Y Chen","year":"2020","journal-title":"J Med Virol"},{"key":"pone.0285093.ref100","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","article-title":"SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor","volume":"181","author":"M. Hoffmann","year":"2020","journal-title":"Cell"},{"key":"pone.0285093.ref101","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s41586-022-04661-w","article-title":"A TMPRSS2 inhibitor acts as a pan-SARS-CoV-2 prophylactic and therapeutic","volume":"605","author":"T Shapira","year":"2022","journal-title":"Nature"},{"issue":"1","key":"pone.0285093.ref102","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1186\/s13063-020-04621-7","article-title":"Pre-exposure prophylaxis with hydroxychloroquine for high-risk healthcare workers during the COVID-19 pandemic: A structured summary of a study protocol for a multicentre, double-blind randomized controlled trial","volume":"21","author":"B Grau-Pujol","year":"2020","journal-title":"Trials"},{"key":"pone.0285093.ref103","unstructured":"Moderna Announces Phase 3 COVE Study of mRNA Vaccine against COVID-19 (mRNA-1273) Begins. Press Release (2020); https:\/\/investors.modernatx.com\/news-releases\/news-release-details\/moderna-announces-phase-3-cove-study-mrna-vaccine-against-covid."},{"key":"pone.0285093.ref104","unstructured":"A Study to Evaluate Efficacy, Safety, and Immunogenicity of mRNA-1273 Vaccine in Adults Aged 18 Years and Older to Prevent COVID-19, ClinicalTrials.gov Identifier: NCT04470427, https:\/\/clinicaltrials.gov\/ct2\/show\/NCT04470427."},{"key":"pone.0285093.ref105","unstructured":"Pfizer and Biotech Choose Lead mRNA Vaccine Candidate against COVID-19 and Commence Pivotal Phase 2\/3 Global Study. Press Release. (2020). https:\/\/www.pfizer.com\/news\/press-release\/press-release-detail\/pfizer-and-biontech-choose-lead-mrna-vaccine-candidate-0"},{"key":"pone.0285093.ref106","article-title":"Safety and Immunogenecity of the ChAdOx1 nCoV-19 Vaccine against SARS-CoV-2: A Preliminary Report of a Phase 1\/2, Single-blind","author":"P Folegatti","year":"2020","journal-title":"Randomized Controlled Trial. The Lancet"},{"key":"pone.0285093.ref107","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1007\/s00281-017-0639-8","article-title":"Cytokine storm and sepsis disease pathogenesis","volume":"39","author":"BG Chousterman","year":"2017","journal-title":"Semin Immunopathol"},{"key":"pone.0285093.ref108","article-title":"The pathogenesis and treatment of the `Cytokine Storm\u2019 in COVID-19","author":"Q Ye","year":"2020","journal-title":"J Infect"},{"issue":"4","key":"pone.0285093.ref109","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/S1473-3099(20)30113-4","article-title":"Viral Load of SARS-CoV-2 in Clinical Samples","volume":"20","author":"Y. Pan","year":"2020","journal-title":"The Lancet"},{"key":"pone.0285093.ref110","article-title":"Asymptomatic Transmission, the Achilles\u2019 Heel of Current Strategies to Control Covid-19","author":"M Gandhi","year":"2020","journal-title":"The New England journal of medicine"},{"key":"pone.0285093.ref111","unstructured":"WHO COVID-19 Rapid Version CRF. https:\/\/bioportal.bioontology.org\/ontologies\/COVIDCRFRAPID Accessed Mar 11 2023."},{"key":"pone.0285093.ref112","unstructured":"COVID-19 Surveillance Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/COVID19 Accessed Mar 11 2023."},{"key":"pone.0285093.ref113","unstructured":"Linked COVID-19 Data Ontology. https:\/\/github.com\/Research-Squirrel-Engineers\/COVID-19. Accessed Mar 11 2023."},{"key":"pone.0285093.ref114","unstructured":"COVID-19 Research Knowledge Graph. https:\/\/github.com\/nasa-jpl-cord-19\/covid19-knowledge-graph. Accessed Mar 11 2023."},{"key":"pone.0285093.ref115","first-page":"122","article-title":"A Community Effort for COVID-19 Ontology Harmonization","author":"AY Lin","year":"2021","journal-title":"The 12th International Conference on Biomedical Ontologies"},{"key":"pone.0285093.ref116","article-title":"Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology","author":"J B everley","year":"2020","journal-title":"Preprint"},{"key":"pone.0285093.ref117","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13326-021-00246-0","article-title":"Toward a systematic conflict resolution framework for ontologies","volume":"12","author":"C.M. Keet","year":"2021","journal-title":"J Biomed Semant"},{"issue":"11","key":"pone.0285093.ref118","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/s41581-020-00335-w","article-title":"Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project","volume":"16","author":"E Ong","year":"2020","journal-title":"Nat Rev Nephrol"},{"issue":"8","key":"pone.0285093.ref119","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.3390\/cancers14081906","article-title":"Ontologies and Knowledge Graphs in Oncology Research","volume":"14","author":"MC Silva","year":"2022","journal-title":"Cancers (Basel)"},{"key":"pone.0285093.ref120","article-title":"Remdesivir for the treatment of Covid-19 \u2010 preliminary report","author":"JH Beigel","year":"2020","journal-title":"N Engl J Med"},{"issue":"1","key":"pone.0285093.ref121","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s12911-023-02136-0","article-title":"Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients","volume":"23","author":"VK Keloth","year":"2023","journal-title":"BMC Med Inform Decis Mak"},{"issue":"7","key":"pone.0285093.ref122","doi-asserted-by":"crossref","first-page":"2229","DOI":"10.1093\/bioinformatics\/btz920","article-title":"Formal axioms in biomedical ontologies improve analysis and interpretation of associated data","volume":"36","author":"FZ Smaili","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0285093.ref123","doi-asserted-by":"crossref","first-page":"i238","DOI":"10.1093\/bioinformatics\/btac256","article-title":"DeepGOZero: improving protein function prediction from sequence and zero- shot learning based on ontology axioms","volume":"38","author":"M Kulmanov","year":"2022","journal-title":"Bioinformatics"},{"key":"pone.0285093.ref124","doi-asserted-by":"crossref","unstructured":"Apolinario-Arzube \u00d3. et al. (2020) CollaborativeHealth: Smart Technologies to Surveil Outbreaks of Infectious Diseases Through Direct and Indirect Citizen Participation. In: Silhavy R. (eds) Applied Informatics and Cybernetics in Intelligent Systems. Advances in Intelligent Systems and Computing. 1226. doi: 10.1007\/978-3-030-51974-2_1","DOI":"10.1007\/978-3-030-51974-2_15"},{"issue":"2","key":"pone.0285093.ref125","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1093\/bib\/bbaa359","article-title":"A review on viral data sources and search systems for perspective mitigation of COVID-19","volume":"22","author":"A Bernasconi","year":"2021","journal-title":"Brief Bioinform"},{"issue":"2","key":"pone.0285093.ref126","doi-asserted-by":"crossref","DOI":"10.1177\/14604582221083850","article-title":"Developing a pneumonia diagnosis ontology from multiple knowledge sources","volume":"28","author":"S Azzi","year":"2022","journal-title":"Health Informatics Journal"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0285093","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T18:36:25Z","timestamp":1705602985000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0285093"}},"subtitle":[],"editor":[{"given":"Barry L.","family":"Bentley","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,1,18]]},"references-count":126,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0285093","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2024,1,18]]}}}