{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T00:39:41Z","timestamp":1777077581143,"version":"3.51.4"},"reference-count":85,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,7,18]],"date-time":"2021-07-18T00:00:00Z","timestamp":1626566400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,7,18]],"date-time":"2021-07-18T00:00:00Z","timestamp":1626566400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["1UL1TR001412"],"award-info":[{"award-number":["1UL1TR001412"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5T15LM012495-03"],"award-info":[{"award-number":["5T15LM012495-03"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5T15LM012495-03"],"award-info":[{"award-number":["5T15LM012495-03"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term <jats:italic>acellular structure<\/jats:italic> to cover viruses and other acellular entities studied by virologists. We now distinguish between <jats:italic>infectious agents<\/jats:italic> \u2013 organisms with an infectious disposition \u2013 and <jats:italic>infectious structures<\/jats:italic> \u2013 acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core\u2019s content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13326-021-00245-1","type":"journal-article","created":{"date-parts":[[2021,7,18]],"date-time":"2021-07-18T08:03:26Z","timestamp":1626595406000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":52,"title":["The Infectious Disease Ontology in the age of COVID-19"],"prefix":"10.1186","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0798-114X","authenticated-orcid":false,"given":"Shane","family":"Babcock","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Beverley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lindsay G.","family":"Cowell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry","family":"Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,7,18]]},"reference":[{"issue":"1","key":"245_CR1","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/2041-1480-5-4","volume":"5","author":"C Pesquita","year":"2014","unstructured":"Pesquita C, Ferreirra JD, Couto FM, Silva MJ. The Epidemiology Ontology: an ontology for the semantic annotation of epidemiological resources. J Biomed Semant. 2014;5(1):4. https:\/\/doi.org\/10.1186\/2041-1480-5-4.","journal-title":"J Biomed Semant"},{"key":"245_CR2","doi-asserted-by":"publisher","unstructured":"Arp R, Smith B, Spear A. Building ontologies with Basic Formal Ontology. Cambridge: MIT Press; 2015. https:\/\/doi.org\/10.7551\/mitpress\/9780262527811.001.0001.","DOI":"10.7551\/mitpress\/9780262527811.001.0001"},{"key":"245_CR3","doi-asserted-by":"publisher","unstructured":"Zeng ML, Hong Y, Clunis J, He S, Coladangelo LP. Implications of Knowledge Organization Systems for Health Information Exchange and Communication during the COVID-19 Pandemic. Data Information Management. 2020;4(3). https:\/\/doi.org\/10.2478\/dim-2020-0009.","DOI":"10.2478\/dim-2020-0009"},{"key":"245_CR4","doi-asserted-by":"publisher","unstructured":"The Gene Ontology Consortium. The Gene Ontology resource: 20 years and still GOing. Nucleic Acids Res. 2019;47(D1):D330\u20138. https:\/\/doi.org\/10.1093\/nar\/gky1055.","DOI":"10.1093\/nar\/gky1055"},{"issue":"11","key":"245_CR5","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25(11):1251\u20135. https:\/\/doi.org\/10.1038\/nbt1346.","journal-title":"Nat Biotechnol"},{"key":"245_CR6","unstructured":"The Open Biomedical Ontologies Foundry. http:\/\/obofoundry.org\/. Accessed 27 Apr 2020."},{"issue":"5","key":"245_CR7","doi-asserted-by":"publisher","first-page":"R46","DOI":"10.1186\/gb-2005-6-5-r46","volume":"6","author":"B Smith","year":"2005","unstructured":"Smith B, Ceusters W, Klagges B, K\u00f6hler J, Kumar A, Lomax J, et al. Relations in biomedical ontologies. Genome Biol. 2005;6(5):R46. https:\/\/doi.org\/10.1186\/gb-2005-6-5-r46.","journal-title":"Genome Biol"},{"key":"245_CR8","unstructured":"ISO\/IEC 21838\u20132. https:\/\/www.iso.org\/standard\/74572.html. Accessed 27 Apr 2020."},{"key":"245_CR9","unstructured":"Basic Formal Ontology (BFO) 2020, https:\/\/basic-formal-ontology.org\/bfo-2020.html. Accessed 2 Mar 2021."},{"key":"245_CR10","doi-asserted-by":"publisher","unstructured":"Cowell LG, Smith B. Infectious disease ontology. In: Sintchenko V, editor. Infectious disease informatics. New York: Springer; 2010:373\u201395. https:\/\/doi.org\/10.1007\/978-1-4419-1327-2_19.","DOI":"10.1007\/978-1-4419-1327-2_19"},{"key":"245_CR11","unstructured":"Goldfain A, Smith B, Cowell LG. 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; 2010. p. 400\u201313."},{"key":"245_CR12","unstructured":"Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. AMIA Summit on Translat Bioinform. 2009; p. 116\u2013120."},{"issue":"7","key":"245_CR13","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1038\/nrmicro2164","volume":"7","author":"M Rupnik","year":"2009","unstructured":"Rupnik M, Wilcox MH, Gerding DN. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol. 2009;7(7):526\u201336. https:\/\/doi.org\/10.1038\/nrmicro2164.","journal-title":"Nat Rev Microbiol"},{"issue":"7","key":"245_CR14","doi-asserted-by":"publisher","first-page":"a017871","DOI":"10.1101\/cshperspect.a017871","volume":"5","author":"J Bruchfeld","year":"2015","unstructured":"Bruchfeld J, Correia-Neves M, K\u00e4llenius G. Tuberculosis and HIV coinfection. Cold Spring Harb Perspect Med. 2015;5(7):a017871. https:\/\/doi.org\/10.1101\/cshperspect.a017871.","journal-title":"Cold Spring Harb Perspect Med"},{"key":"245_CR15","doi-asserted-by":"publisher","unstructured":"Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, et al. The Ontology for Biomedical Investigations. PLoS One. 2016;11(4):e0154556. https:\/\/doi.org\/10.1371\/journal.pone.0154556.","DOI":"10.1371\/journal.pone.0154556"},{"key":"245_CR16","unstructured":"https:\/\/github.com\/obi-ontology\/obi\/issues\/1306. Accessed 4 Mar 2021."},{"key":"245_CR17","doi-asserted-by":"publisher","unstructured":"Federhen S. The NCBI Taxonomy Database. Nucleic Acids Res. 2012; 40:D136-D143. doi:https:\/\/doi.org\/10.1093\/nar\/gkr1178","DOI":"10.1093\/nar\/gkr1178"},{"issue":"3","key":"245_CR18","doi-asserted-by":"publisher","first-page":"261","DOI":"10.3201\/eid0303.970302","volume":"3","author":"JM McNicholl","year":"1997","unstructured":"McNicholl JM, Smith DK, Qari SH, Hodge T. Host genes and HIV: The role of the chemokine receptor gene CCR5 and its allele (\u220632 CCR5). Emerg Infect Dis. 1997;3(3):261\u201371. https:\/\/doi.org\/10.3201\/eid0303.970302.","journal-title":"Emerg Infect Dis"},{"key":"245_CR19","unstructured":"Pathogen Transmission Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/PTRANS. Accessed 27 Apr 2020."},{"issue":"1","key":"245_CR20","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.jbi.2010.02.008","volume":"44","author":"A Goldfain","year":"2011","unstructured":"Goldfain A, Smith B, Cowell LG. Towards an ontological representation of resistance: the case of MRSA. J Biomed Inform. 2011;44(1):35\u201341. https:\/\/doi.org\/10.1016\/j.jbi.2010.02.008.","journal-title":"J Biomed Inform"},{"key":"245_CR21","doi-asserted-by":"publisher","unstructured":"Hogan WR, Wagner MM, Brochhausen M, Levander J, Brown ST, Millet N. The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. J Biomed Semant. 2016; 7(50). doi:https:\/\/doi.org\/10.1186\/s13326-016-0092-y.","DOI":"10.1186\/s13326-016-0092-y"},{"key":"245_CR22","unstructured":"Ceusters W, Smith B. About: towards foundations for the Information Artifact Ontology. In: Couto FM, Hasting J, editors. Proceedings of the 6th International Conference on Biomedical Ontology (ICBO 2015). CEUR-WS.org; 2015:1\u20135."},{"key":"245_CR23","doi-asserted-by":"publisher","unstructured":"Liu Y, Chan W, Wang Z, Hur J, Xie J, Yu H, et al. Ontological and bioinformatic analysis of anti-coronavirus drugs and their implication for drug repurposing against COVID-19. Preprints. https:\/\/doi.org\/10.20944\/preprints202003.0413.v1 (2020). Accessed 27 Apr 2020.","DOI":"10.20944\/preprints202003.0413.v1"},{"key":"245_CR24","doi-asserted-by":"publisher","unstructured":"Ong E, Wong M, Huffman A, He Y. COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning. bioRxiv. https:\/\/doi.org\/10.1101\/2020.03.20.000141 (2020). Accessed 27 April 2020.","DOI":"10.1101\/2020.03.20.000141"},{"key":"245_CR25","doi-asserted-by":"publisher","unstructured":"He Y, Yu H, Ong E, Wang Y, Liu Y, Huffman A, et al. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Sci Data. 2020; 7(181). doi:https:\/\/doi.org\/10.1038\/s41597-020-0523-6.","DOI":"10.1038\/s41597-020-0523-6"},{"key":"245_CR26","unstructured":"Coronavirus Infectious Disease Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/CIDO. Accessed 27 Apr 2020."},{"key":"245_CR27","unstructured":"Luciano J, Schriml L, Squires B, Scheuermann R. The Influenza Infectious Disease Ontology (I-IDO). The 11th Annual Bio-Ontologies Meeting, ISMB. 2008, 20 July; Toronto, Canada."},{"key":"245_CR28","unstructured":"Influenza Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/FLU. Accessed 27 Apr 2020."},{"issue":"1","key":"245_CR29","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/2041-1480-2-9","volume":"2","author":"Y Lin","year":"2011","unstructured":"Lin Y, Xiang Z, He Y. Brucellosis ontology (IDOBRU) as an extension of the infectious disease ontology. J Biomed Semant. 2011;2(1):9. https:\/\/doi.org\/10.1186\/2041-1480-2-9.","journal-title":"J Biomed Semant."},{"key":"245_CR30","unstructured":"Brucellosis Ontology. https:\/\/ bioportal.bioontology.org\/ontologies\/IDOBRU. Accessed 27 Apr 2020."},{"key":"245_CR31","doi-asserted-by":"crossref","unstructured":"Beverley J, Smith B, Babcock S, Cowell L. Coordinating coronavirus research: the COVID-19 Infectious Disease Ontology. OSF Preprints. https:\/\/osf.io\/5bx8c\/ (2020). Accessed 20 Sept 2020.","DOI":"10.31219\/osf.io\/5bx8c"},{"key":"245_CR32","unstructured":"Virus Infectious Disease Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/VIDO. Accessed 15 Jun 2020."},{"key":"245_CR33","unstructured":"COVID-19 Infectious Disease Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/IDO-COVID-19. Accessed 15 Jun 2020."},{"issue":"2","key":"245_CR34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0003479","volume":"9","author":"E Mitraka","year":"2015","unstructured":"Mitraka E, Topalis P, Dritsou V, Dialynas E, Louis C. Describing the breakbone fever: IDODEN, an ontology for dengue fever. PLoS Negl Trop Dis. 2015;9(2):e0003479. https:\/\/doi.org\/10.1371\/journal.pntd.0003479.","journal-title":"PLoS Negl Trop Dis"},{"key":"245_CR35","unstructured":"Dengue Fever Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/IDODEN. Accessed 27 Apr 2020."},{"key":"245_CR36","doi-asserted-by":"publisher","unstructured":"Topalis P, Mitraka E, Bujila I, Deligianni E, Dialynas E, Siden-Kiamos I, et al. IDOMAL: an ontology for malaria. Malar J. 2010; 9(230). doi:https:\/\/doi.org\/10.1186\/1475-2875-9-230.","DOI":"10.1186\/1475-2875-9-230"},{"key":"245_CR37","unstructured":"Malaria Ontology. https:\/\/github.com\/VeuPathDB-ontology\/IDOMAL. Accessed 27 Apr 2020."},{"key":"245_CR38","unstructured":"B\u00e9r\u00e9 C, Camara G, Malo S, Lo M, Ouaro S. IDOMEN: an extension of Infectious Disease Ontology for MENingitis. In: Ohno-Machado L, S\u00e9roussi B, editors. MEDINFO 2019: health and wellbeing e-networks for all. Amsterdam: IOS Press; 2019. p. 313\u20137."},{"key":"245_CR39","unstructured":"Meningitis Ontology. https:\/\/github.com\/cedricbere\/IDOMEN. Accessed 27 Apr 2020."},{"key":"245_CR40","unstructured":"Walls RL, Smith B, Elser J, Goldfain A, Stevenson DW, Jaiswal P. A plant disease extension of the Infectious Disease Ontology. In: Cornet R, Stevens R, editors. Proceedings of the 3rd International Conference on Biomedical Ontology. CEURS-WS.org; 2012. P. 1\u20135."},{"key":"245_CR41","unstructured":"Plant Disease Ontology. http:\/\/purl.obolibrary.org\/obo\/idoplant.owl. Accessed 27 Apr 2020."},{"key":"245_CR42","unstructured":"Goldfain A, Smith B, Cowell LG. Constructing a lattice of infectious disease ontologies from a Staphylococcus aureus isolate repository. In: Cornet R, Stevens R, editors. Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012). CEURS-WS.org; 2012. P. 1\u20135."},{"key":"245_CR43","unstructured":"Staphylococcus aureus Infectious Disease Ontology. https:\/\/github.com\/awqbi\/ido-staph. Accessed 27 Apr 2020."},{"key":"245_CR44","unstructured":"Camara G, Despr\u00e8s S, Lo M. IDOSCHISTO: une extension de l\u2019ontologie noyau des maladies infectieuses (IDO-Core) pour la schistosomiases. In: Faron-Zucker C, editor. IC \u2013 25\u00e8mes Journ\u00e9es francophones d\u2019Ing\u00e9nierie des Connaissances, Clermont-Ferrand, France. Session 1: Construction, peuplement et exploitation d\u2019ontologies. 2014. P. 39\u201350."},{"key":"245_CR45","unstructured":"Schistosomiasis Ontology. https:\/\/github.com\/gaoussoucamara\/idoschisto. Accessed 27 Apr 2020."},{"issue":"6","key":"245_CR46","doi-asserted-by":"publisher","first-page":"e98810","DOI":"10.1371\/journal.pone.0098810","volume":"9","author":"D Sargeant","year":"2014","unstructured":"Sargeant D, Deverasetty S, Strong CL, Alaniz IJ, Bartlett A, Brandon NR, et al. The HIVToolbox 2 web system integrates sequence, structure, Function and Mutation Analysis. PLOS ONE. 2014;9(6):e98810. https:\/\/doi.org\/10.1371\/journal.pone.0098810.","journal-title":"PLOS ONE"},{"key":"245_CR47","unstructured":"HIV Ontology. https:\/\/ bioportal.bioontology.org\/ontologies\/HIV. Accessed 27 Apr 2020."},{"key":"245_CR48","unstructured":"Network on Antimicrobial Resistance in Staphylococcus aureus. http:\/\/www.narsa.net\/. Accessed 27 Apr 2020."},{"key":"245_CR49","doi-asserted-by":"publisher","unstructured":"Kuhn J. Virus Taxonomy. Reference Modules in Life Sciences. 2020. https:\/\/doi.org\/10.1016\/B978-0-12-809633-8.21231-4.","DOI":"10.1016\/B978-0-12-809633-8.21231-4"},{"issue":"1","key":"245_CR50","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/1756-0500-3-175","volume":"3","author":"Z Xiang","year":"2010","unstructured":"Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: webbased support for ontology reuse. BMC research notes. 2010;3(1):175. https:\/\/doi.org\/10.1186\/1756-0500-3-175.","journal-title":"BMC research notes"},{"key":"245_CR51","doi-asserted-by":"publisher","unstructured":"Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, et al. Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 2009; 10(125). doi:https:\/\/doi.org\/10.1186\/1471-2105-10-125.","DOI":"10.1186\/1471-2105-10-125"},{"issue":"3","key":"245_CR52","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1128\/br.35.3.235-241.1971","volume":"35","author":"D Baltimore","year":"1971","unstructured":"Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971;35(3):235\u201341. https:\/\/doi.org\/10.1128\/br.35.3.235-241.1971.","journal-title":"Bacteriol Rev"},{"key":"245_CR53","unstructured":"Symptom Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/SYMP. Accessed 3 Aug 2020."},{"key":"245_CR54","unstructured":"Coronavirus disease 2019 (COVID-19) 2020 interim case Definition, approved April 2, 2020. Centers for Disease Control and Prevention 2020; https:\/\/wwwn.cdc.gov\/nndss\/conditions\/coronavirus-disease-2019-covid-19\/case-definition\/2020\/. Accessed 3 Aug 2020."},{"key":"245_CR55","unstructured":"Standardization Surveillance Case Definition and National Notification for 2019 Coronavirus disease (COVID-19). Council of State of Territorial Epidemiologists 2020; https:\/\/asprtracie.hhs.gov\/technical-resources\/resource\/8322\/standardized-surveillance-case-definition-and-national-notification-for-2019-novel-coronavirus-disease-covid-19. Accessed 3 Aug 2020."},{"key":"245_CR56","doi-asserted-by":"publisher","unstructured":"Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y, et al. Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res. 2019;47(D1):D693\u2013700. https:\/\/doi.org\/10.1093\/nar\/gky999.","DOI":"10.1093\/nar\/gky999"},{"key":"245_CR57","doi-asserted-by":"publisher","unstructured":"Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F. Network-based Drug Repurposing for Novel Coronavirus 2019-nCoV\/SARS-CoV-2. Cell Discovery. 2020; 6(14). doi:https:\/\/doi.org\/10.1038\/s41421-020-0153-3.","DOI":"10.1038\/s41421-020-0153-3"},{"issue":"Database","key":"245_CR58","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkm791","volume":"36","author":"K Degtyarenko","year":"2008","unstructured":"Degtyarenko K, Matos P, Ennis M, Hastings J, Zbinden M, Mcnaught A, et al. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2008;36(Database):D344\u201350. https:\/\/doi.org\/10.1093\/nar\/gkm791.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"245_CR59","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/2041-1480-5-21","volume":"5","author":"MA Haendel","year":"2014","unstructured":"Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, et al. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semant. 2014;5(1):21. https:\/\/doi.org\/10.1186\/2041-1480-5-21.","journal-title":"J Biomed Semant."},{"key":"245_CR60","doi-asserted-by":"crossref","unstructured":"He Y, Cowell LG, Diehl AD, Mobley H, Peters B, Ruttenberg A, et al. VO: Vaccine Ontology. In: Smith B, editor. Proceedings of the 1st International Conference on Biomedical Ontology (ICBO 2009). Buffalo: NCOR; 2009. P. 172.69.","DOI":"10.1038\/npre.2009.3553"},{"issue":"1","key":"245_CR61","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1146\/annurev-virology-110615-042301","volume":"3","author":"F Li","year":"2016","unstructured":"Li F. Structure, function, and evolution of coronavirus spike proteins. Annu Rev Virol. 2016;3(1):237\u201361. https:\/\/doi.org\/10.1146\/annurev-virology-110615-042301.","journal-title":"Annu Rev Virol"},{"key":"245_CR62","doi-asserted-by":"publisher","unstructured":"Schoeman D, Fielding BC. Coronavirus envelope protein: current knowledge. Virol J. 2019; 16(69). doi: https:\/\/doi.org\/10.1186\/s12985-019-1182-0.","DOI":"10.1186\/s12985-019-1182-0"},{"issue":"4","key":"245_CR63","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1038\/s41564-020-0688-y","volume":"5","author":"M Letko","year":"2020","unstructured":"Letko M, Marzi A, Munster V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat Microbiol. 2020;5(4):562\u20139. https:\/\/doi.org\/10.1038\/s41564-020-0688-y.","journal-title":"Nat Microbiol"},{"issue":"4","key":"245_CR64","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1002\/jmv.2568","volume":"92","author":"Y Chen","year":"2020","unstructured":"Chen Y, Liu Q, Guo D. Emerging coronaviruses: genome structure, replication, and pathogenesis. J Med Virol. 2020;92(4):418\u201323. https:\/\/doi.org\/10.1002\/jmv.2568.","journal-title":"J Med Virol"},{"key":"245_CR65","doi-asserted-by":"publisher","unstructured":"Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen S, et al. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 2017;45(D1):D339\u201346. https:\/\/doi.org\/10.1093\/nar\/gkw1075.","DOI":"10.1093\/nar\/gkw1075"},{"key":"245_CR66","doi-asserted-by":"publisher","unstructured":"Hoffmann M, Kleine-Weber H, Schroeder S, Kr\u00fcger N, Herrler T, Erichsen S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181(2):271\u201380 e278. https:\/\/doi.org\/10.1016\/j.cell.2020.02.052.","DOI":"10.1016\/j.cell.2020.02.052"},{"key":"245_CR67","unstructured":"WHO COVID-19 Rapid Version CRF. https:\/\/bioportal.bioontology.org\/ ontologies\/COVIDCRFRAPID. Accessed 27 Apr 2020."},{"key":"245_CR68","unstructured":"COVID-19 Surveillance Ontology. https:\/\/bioportal.bioontology.org\/ontologies\/COVID19. Accessed 27 Apr 2020."},{"key":"245_CR69","unstructured":"Linked COVID-19 Data Ontology. https:\/\/github.com\/Research-Squirrel-Engineers\/COVID-19. Accessed 27 Apr 2020."},{"key":"245_CR70","unstructured":"COVID-19 Research Knowledge Graph. https:\/\/github.com\/nasa-jpl-cord-19\/covid19-knowledge-graph. Accessed 27 Apr 2020."},{"key":"245_CR71","first-page":"529","volume-title":"Biological Data Mining","author":"R Scheuermann","year":"2009","unstructured":"Scheuermann R, Kong M, Dahlke C, Cai J, Lee J, Qian Y, et al. Ontology-based knowledge representation of experiment metadata in biological data mining. In: Chen J, Lonardi S, editors. Biological Data Mining. Boca Raton, FL: Chapman & Hall; 2009. p. 529\u201359."},{"key":"245_CR72","doi-asserted-by":"publisher","unstructured":"Schriml L, Chuvochina M, Davies N, Eloe-Fadrosh, E, Finn R, Hugenholtz P, et al. COVID-19 pandemic reveals the peril of ignoring metadata standards. Sci Data. 2020; 7(188). doi:https:\/\/doi.org\/10.1038\/s41597-020-0524-5.","DOI":"10.1038\/s41597-020-0524-5"},{"key":"245_CR73","unstructured":"National Library of Medicine. https:\/\/www.nlm.nih.gov\/. Accessed 20 Sept 2020."},{"key":"245_CR74","doi-asserted-by":"publisher","unstructured":"Liu-Wei W, Kafkas \u015e, Chen J, Tegn\u00e9r J, Hoehndorf R. Prediction of novel virus\u2013host interactions by integrating clinical symptoms and protein sequences. bioRxiv. https:\/\/doi.org\/10.1101\/2020.04.22.055095 (2020). Accessed 27 Apr 2020.","DOI":"10.1101\/2020.04.22.055095"},{"key":"245_CR75","doi-asserted-by":"publisher","unstructured":"Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, et al. The GOA database: Gene Ontology annotation updates for 2015. Nucleic Acids Res. 2015;43(D1):D1057\u201363. https:\/\/doi.org\/10.1093\/nar\/gku1113.","DOI":"10.1093\/nar\/gku1113"},{"key":"245_CR76","doi-asserted-by":"publisher","unstructured":"Squires RB, Noronha J, Hunt V, Garc\u00eda-Sastre A, Macken C, Baumgarth N, et al. Influenza research database: an integrated bioinformatics resource for influenza virus research. Influenza Other Respir Viruses. 2012;6(6):404\u201316. https:\/\/doi.org\/10.1111\/j.1750-2659.2011.00331.x.","DOI":"10.1111\/j.1750-2659.2011.00331.x"},{"key":"245_CR77","doi-asserted-by":"publisher","unstructured":"Kulmanov M, Smaili FZ, Gao X, Hoehndorf R, Machine learning with biomedical ontologies. bioRxiv. https:\/\/doi.org\/10.1101\/2020.05.07.082164 (2020). Accessed 15 Jul 2020.","DOI":"10.1101\/2020.05.07.082164"},{"key":"245_CR78","unstructured":"BFO 2.0 Users Guide. http:\/\/purl.obolibrary.org\/obo\/bfo\/Reference. Accessed 17 Apr 2021."},{"key":"245_CR79","unstructured":"https:\/\/www.youtube.com\/channel\/UC8rDbmRGP6A2bs6tn0AOErQ. Accessed 17 Apr 2021."},{"key":"245_CR80","unstructured":"BFO Discussion Group. https:\/\/groups.google.com\/g\/bfo-discuss. Accessed 17 Apr 2021."},{"key":"245_CR81","unstructured":"https:\/\/github.com\/OBOFoundry\/OBOFoundry.github.io\/issues. Accessed 17 Apr 2021."},{"key":"245_CR82","unstructured":"https:\/\/obo-communitygroup.slack.com\/?redir=%2Farchives%2FC01DP18L5GW. Accessed 17 Apr 2021."},{"key":"245_CR83","unstructured":"https:\/\/github.com\/infectious-disease-ontology-extensions. Accessed 20 Feb 2020."},{"key":"245_CR84","unstructured":"Prot\u00e9g\u00e9. http:\/\/protege.stanford.edu. Accessed 27 Apr 2020."},{"key":"245_CR85","unstructured":"https:\/\/github.com\/infectious-disease-ontology\/infectious-disease-ontology. Accessed 27 Apr 2020."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-021-00245-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-021-00245-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-021-00245-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,18]],"date-time":"2021-07-18T08:11:36Z","timestamp":1626595896000},"score":1,"resource":{"primary":{"URL":"https:\/\/jbiomedsem.biomedcentral.com\/articles\/10.1186\/s13326-021-00245-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,18]]},"references-count":85,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["245"],"URL":"https:\/\/doi.org\/10.1186\/s13326-021-00245-1","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,18]]},"assertion":[{"value":"31 May 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 June 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"13"}}