{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T17:34:44Z","timestamp":1754156084451,"version":"3.41.2"},"reference-count":37,"publisher":"Emerald","issue":"5\/6","license":[{"start":{"date-parts":[[2022,10,5]],"date-time":"2022-10-05T00:00:00Z","timestamp":1664928000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.emerald.com\/insight\/site-policies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJWIS"],"published-print":{"date-parts":[[2022,12,12]]},"abstract":"<jats:sec>\n<jats:title content-type=\"abstract-subheading\">Purpose<\/jats:title>\n<jats:p>The purpose of this paper is to describe the CODO ontology (COviD-19 Ontology) that captures epidemiological data about the COVID-19 pandemic in a knowledge graph that follows the FAIR principles. This study took information from spreadsheets and integrated it into a knowledge graph that could be queried with SPARQL and visualized with the Gruff tool in AllegroGraph.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title content-type=\"abstract-subheading\">Design\/methodology\/approach<\/jats:title>\n<jats:p>The knowledge graph was designed with the Web Ontology Language. The methodology was a hybrid approach integrating the YAMO methodology for ontology design and Agile methods to define iterations and approach to requirements, testing and implementation.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title content-type=\"abstract-subheading\">Findings<\/jats:title>\n<jats:p>The hybrid approach demonstrated that Agile can bring the same benefits to knowledge graph projects as it has to other projects. The two-person team went from an ontology to a large knowledge graph with approximately 5\u2009M triples in a few months. The authors gathered useful real-world experience on how to most effectively transform \u201cfrom strings to things.\u201d<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title content-type=\"abstract-subheading\">Originality\/value<\/jats:title>\n<jats:p>This study is the only FAIR model (to the best of the authors\u2019 knowledge) to address epidemiology data for the COVID-19 pandemic. It also brought to light several practical issues that generalize to other studies wishing to go from an ontology to a large knowledge graph. This study is one of the first studies to document how the Agile approach can be used for knowledge graph development.<\/jats:p>\n<\/jats:sec>","DOI":"10.1108\/ijwis-03-2022-0047","type":"journal-article","created":{"date-parts":[[2022,10,4]],"date-time":"2022-10-04T00:41:03Z","timestamp":1664844063000},"page":"432-452","source":"Crossref","is-referenced-by-count":4,"title":["From ontology to knowledge graph with agile methods: the case of COVID-19 CODO knowledge graph"],"prefix":"10.1108","volume":"18","author":[{"given":"Michael","family":"DeBellis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Biswanath","family":"Dutta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"140","published-online":{"date-parts":[[2022,10,5]]},"reference":[{"year":"2011","key":"key2022120904442965200_ref001","article-title":"RDF browser for data discovery and visual query building"},{"issue":"1","key":"key2022120904442965200_ref002","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1177\/1740774507087602","article-title":"The impact of privacy and confidentiality laws on the conduct of clinical trials","volume":"5","year":"2008","journal-title":"Clinical Trials"},{"volume-title":"Building Ontologies with Basic Formal Ontology","year":"2015","key":"key2022120904442965200_ref003"},{"issue":"4","key":"key2022120904442965200_ref004","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1111\/tbed.13892","article-title":"Interoperable medical data: the missing link for understanding COVID-19","volume":"68","year":"2021","journal-title":"Transboundary and Emerging Diseases"},{"volume-title":"Extreme Programming Explained: Embrace Change","year":"2000","key":"key2022120904442965200_ref005"},{"issue":"5","key":"key2022120904442965200_ref006","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1109\/2.59","article-title":"A spiral model of software development and enhancement","volume":"21","year":"1988","journal-title":"Computer"},{"issue":"1","key":"key2022120904442965200_ref007","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1146\/annurev-biodatasci-010820-091627","article-title":"Knowledge-based biomedical data science","volume":"3","year":"2020","journal-title":"Annual Review of Biomedical Data Science"},{"issue":"8","key":"key2022120904442965200_ref008","first-page":"47","article-title":"COVID-19 ontology evaluation","volume":"11","year":"2020","journal-title":"International Journal of Management"},{"key":"key2022120904442965200_ref009","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-1327-2_19","article-title":"Infectious disease ontology","volume-title":"Infectious Disease Informatics","year":"2010"},{"key":"key2022120904442965200_ref010","unstructured":"DeBellis, M. (2020), \u201cLisp and SPARQL files for CODO ontology\u201d, available at: https:\/\/github.com\/mdebellis\/CODO-Lisp (accessed 28 February 2022)."},{"issue":"9","key":"key2022120904442965200_ref011","doi-asserted-by":"publisher","first-page":"1332","DOI":"10.1101\/2020.04.14.040667","article-title":"COVID-19 knowledge graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology","volume":"37","year":"2020","journal-title":"Bioinformatics"},{"year":"2020","key":"key2022120904442965200_ref012","article-title":"CODO: an ontology for collection and analysis of COVID-19 data"},{"issue":"1","key":"key2022120904442965200_ref013","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1108\/JKM-10-2014-0439","article-title":"YAMO: yet another methodology for large-scale faceted ontology construction","volume":"19","year":"2015","journal-title":"Journal of Knowledge Management"},{"key":"key2022120904442965200_ref014","unstructured":"Falbo, R. (2014), \u201cSABiO: Systematic approach for building ontologies\u201d, Technical Report, Ontology and Conceptual Modeling Research Group (NEMO), Federal University of Esp\u00edrito Santo, Vit\u00f3ria, Brazil."},{"key":"key2022120904442965200_ref015","unstructured":"Franz Inc (2022a), \u201cAllegroGraph 7.2.0 materialized reasoner\u201d, available at: https:\/\/franz.com\/agraph\/support\/documentation\/current\/materializer.html (accessed 28 February 2022)."},{"key":"key2022120904442965200_ref016","unstructured":"Franz Inc (2022b), \u201cAllegroGraph freetext indexing\u201d, available at: https:\/\/franz.com\/agraph\/support\/documentation\/current\/text-index.html (accessed 28 February 2022)."},{"year":"2009","key":"key2022120904442965200_ref017","article-title":"Developing ontologies within decentralized settings"},{"key":"key2022120904442965200_ref018","unstructured":"Gardner, L. (2020), \u201cModeling the spreading risk of 2019-nCoV\u201d, available at: https:\/\/systems.jhu.edu\/research\/public-health\/ncov-model-2\/ (accessed 28 February 2022)."},{"key":"key2022120904442965200_ref019","doi-asserted-by":"publisher","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","volume":"7","year":"2020","journal-title":"Science Data"},{"key":"key2022120904442965200_ref020","doi-asserted-by":"crossref","unstructured":"Keet, M. (2011), \u201cThe use of foundational ontologies in ontology development: an empirical assessment\u201d, Technical Report, KRDB Research Centre, Free University of Bozen-Bolzano, Italy.","DOI":"10.1007\/978-3-642-21034-1_22"},{"article-title":"Knowledge graphs and COVID-19: opportunities, challenges, and implementation","year":"2020","key":"key2022120904442965200_ref021","doi-asserted-by":"publisher","DOI":"10.1162\/99608f92.e45650b8"},{"volume-title":"Knowledge Acquisition for Expert Systems: A Practical Handbook","year":"1987","key":"key2022120904442965200_ref022"},{"edition":"1st ed.","volume-title":"The Rational Unified Process Made Easy: A Practitioner\u2019s Guide to the RUP","year":"2003","key":"key2022120904442965200_ref023"},{"year":"2021","key":"key2022120904442965200_ref024","article-title":"A community effort for COVID-19 ontology harmonization"},{"key":"key2022120904442965200_ref025","unstructured":"Mullins, C. (2020), \u201cExtract, load, transform (ELT)\u201d, January 2020, Published by TechTarget.com, Newton, Massachusetts, available at: www.techtarget.com\/searchdatamanagement\/definition\/Extract-Load-Transform-ELTAccessedon:27-6-2022"},{"issue":"4","key":"key2022120904442965200_ref026","article-title":"The prot\u00e9g\u00e9 project: a look back and a look forward","volume":"1","year":"2015","journal-title":"AI Matters"},{"year":"2010","key":"key2022120904442965200_ref027","article-title":"Mapping master: a flexible approach for mapping spreadsheets to owl"},{"key":"key2022120904442965200_ref028","unstructured":"Pallozzi, D. (2018), \u201cThe word that took the tech world by storm: returning to the roots of agile\u201d, ThoughtWorks white paper, available at: www.thoughtworks.com\/perspectives\/edition1-agile-article (accessed 28 February 2022)."},{"key":"key2022120904442965200_ref029","unstructured":"Singhal, A. (2012), \u201cIntroducing the knowledge graph: things, not strings\u201d, Google white paper available at: www.blog.google\/products\/search\/introducing-knowledge-graph-things-not\/ (accessed 28 February 2022)."},{"key":"key2022120904442965200_ref030","unstructured":"Sirin, E. (2020), \u201cAnalyzing COVID-19 data with SPARQL\u201d, available at: www.stardog.com\/labs\/blog\/analyzing-covid-19-data-with-sparql\/ (accessed 28 February 2022)."},{"issue":"2","key":"key2022120904442965200_ref031","doi-asserted-by":"crossref","first-page":"ooab036","DOI":"10.1093\/jamiaopen\/ooab036","article-title":"Development of a coronavirus disease 2019 (COVID-19) application ontology for the accrual to clinical trials (ACT) network","volume":"4","year":"2021","journal-title":"JAMIA Open"},{"key":"key2022120904442965200_ref032","unstructured":"W3C (2004), \u201cSWRL: a semantic web rule language combining OWL and RuleML\u201d, W3C Member Submission, available at: www.w3.org\/Submission\/SWRL\/ (accessed 28 February 2022)."},{"issue":"1","key":"key2022120904442965200_ref033","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","year":"2016","journal-title":"Scientific Data"},{"key":"key2022120904442965200_ref034","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.sbi.2021.09.003","article-title":"Toward better drug discovery with knowledge graphs","volume":"72","year":"2022","journal-title":"Current Opinion in Structural Biology"},{"key":"key2022120904442965200_ref035","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1145\/1385989.1386007","article-title":"Unification of geospatial reasoning, temporal logic, and social network analysis in event-based systems","year":"2008"},{"key":"key2022120904442965200_ref036","first-page":"153","article-title":"Developing the Covid-19 CODO knowledge graph: an agile approach from ontology to knowledge graph","volume-title":"Knowledge Graphs and Semantic Web. KGSWC 2021. Communications in Computer and Information Science (CCIS)","year":"2021"},{"volume-title":"Knowledge Graphs and Semantic Web","year":"2020","key":"key2022120904442965200_ref037"}],"container-title":["International Journal of Web Information Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.emerald.com\/insight\/content\/doi\/10.1108\/IJWIS-03-2022-0047\/full\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.emerald.com\/insight\/content\/doi\/10.1108\/IJWIS-03-2022-0047\/full\/html","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,24]],"date-time":"2025-07-24T22:23:52Z","timestamp":1753395832000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.emerald.com\/ijwis\/article\/18\/5-6\/432-452\/445222"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,5]]},"references-count":37,"journal-issue":{"issue":"5\/6","published-online":{"date-parts":[[2022,10,5]]},"published-print":{"date-parts":[[2022,12,12]]}},"alternative-id":["10.1108\/IJWIS-03-2022-0047"],"URL":"https:\/\/doi.org\/10.1108\/ijwis-03-2022-0047","relation":{},"ISSN":["1744-0084","1744-0084"],"issn-type":[{"type":"print","value":"1744-0084"},{"type":"electronic","value":"1744-0084"}],"subject":[],"published":{"date-parts":[[2022,10,5]]}}}