{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:18:11Z","timestamp":1790086691210,"version":"4.0.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,11,28]],"date-time":"2017-11-28T00:00:00Z","timestamp":1511827200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,11,28]],"date-time":"2017-11-28T00:00:00Z","timestamp":1511827200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100004054","name":"King Abdulaziz University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different \u201cformalisms\u201d to represent and share their data \u2013 by the far most common, however, is the \u201coffice file\u201d either in the form of a word-processor document or a spreadsheet.<\/jats:p>\n                    <jats:p>Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-017-0159-4","type":"journal-article","created":{"date-parts":[[2017,11,27]],"date-time":"2017-11-27T19:54:50Z","timestamp":1511812490000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A document-centric approach for developing the tolAPC ontology"],"prefix":"10.1186","volume":"8","author":[{"given":"Aisha","family":"Blfgeh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Warrender","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catharien M. U.","family":"Hilkens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip","family":"Lord","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,11,28]]},"reference":[{"key":"159_CR1","doi-asserted-by":"crossref","unstructured":"Bernus P, Shaw MJ. International Handbooks on Information Systems.2007. p. 654. doi:10.1007\/978-3-642-00416-2. http:\/\/www.gbv.de\/du\/services\/toc\/bs\/368354474.","DOI":"10.1007\/978-3-642-00416-2"},{"issue":"4","key":"159_CR2","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1093\/bib\/1.4.398","volume":"1","author":"R Stevens","year":"2000","unstructured":"Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinform. 2000; 1(4):398\u2013414. doi:10.1093\/bib\/1.4.398.","journal-title":"Brief Bioinform"},{"key":"159_CR3","unstructured":"Bada M, Stevens R, Goble C, Gil Y, Ashburner M, Blake JA, Cherry JM, Harris M, Lewis S. The Gene Ontology: What It Is (and What It Isn\u2019t). 2015. http:\/\/www.cs.man.ac.uk\/%7Estevensr\/papers\/go-web-semantics.pdf. Accessed 14 Dec 2015."},{"key":"159_CR4","unstructured":"World Health Organization. WHO International Classification of Diseases (ICD): World Health Organization; 2016. http:\/\/www.who.int\/classifications\/icd\/en\/. Accessed 8 June 2016."},{"key":"159_CR5","unstructured":"IHTSDO. International Health Terminology Standards Development Organisation 2016. http:\/\/www.ihtsdo.org\/snomed-ct\/. Accessed 17 June 2016."},{"key":"159_CR6","unstructured":"Lord P. The Semantic Web takes Wing: Programming Ontologies with Tawny-OWL. OWLED 2013. 2013. Accessed 4 Mar 2013."},{"issue":"2","key":"159_CR7","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/j.websem.2003.12.003","volume":"1","author":"M Bada","year":"2004","unstructured":"Bada M, Stevens R, Goble C, Gil Y, Ashburner M, Blake JA, Cherry M, Harris M, Lewis S. A Short Study on the Success of Gene Ontology. Web Semant Sci Serv Agents World Wide Web. 2004; 1(2):235\u201340. doi:10.1016\/j.websem.2003.12.003.","journal-title":"Web Semant Sci Serv Agents World Wide Web"},{"key":"159_CR8","doi-asserted-by":"crossref","unstructured":"Garcia A, O\u2019Neill K, Garcia LJ, Lord P, Stevens R, Corcho O, Gibson F. Developing ontologies within decentralised settings In: Chen H, Wang Y, Cheung K-H, editors. Semantic e-Science. Springer: 2010. p. 99\u2013140. http:\/\/precedings.nature.com\/documents\/3231\/version\/1\/html.","DOI":"10.1007\/978-1-4419-5908-9_4"},{"key":"159_CR9","doi-asserted-by":"crossref","unstructured":"Wood A, Flowerdew J, Peacock M. International scientific english: The language of research scientists around the world. Res Perspect Engl Acad Purp. 2001:71\u201383. doi:10.1017\/cbo9781139524766.008.","DOI":"10.1017\/CBO9781139524766.008"},{"issue":"4","key":"159_CR10","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1145\/2757001.2757003","volume":"1","author":"MA Musen","year":"2015","unstructured":"Musen MA, Team tP. The prot\u00e9g\u00e9 project: A look back and a look forward. AI Matters. 2015; 1(4):4\u201312. doi:10.1145\/2757001.2757003.","journal-title":"AI Matters"},{"issue":"1","key":"159_CR11","first-page":"89","volume":"4","author":"T Tudorache","year":"2013","unstructured":"Tudorache T, Nyulas C, Noy NF, Musen MA. Webprot\u00e9g\u00e9: A collaborative ontology editor and knowledge acquisition tool for the web. Semant Web. 2013; 4(1):89\u201399. doi:10.3233\/SW-2012-0057.","journal-title":"Semant Web"},{"key":"159_CR12","unstructured":"Tudorache T, Nyulas CI, Noy NF, Redmond T, Musen M. iCAT: A Collaborative Authoring Tool for ICD-11. Proc ISWC 2011 Work Ontologies Come Age Semant Web (OCAS). 2011. http:\/\/ceur-ws.org\/Vol-809\/paper-09.pdf. Accessed 10 Apr 2016."},{"key":"159_CR13","doi-asserted-by":"crossref","unstructured":"O\u2019Connor MJ, Halaschek-Wiener C, Musen MA. Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. In: 9th International Semantic Web Conference (ISWC): 2010.","DOI":"10.1007\/978-3-642-17749-1_13"},{"issue":"14","key":"159_CR14","doi-asserted-by":"publisher","first-page":"2021","DOI":"10.1093\/bioinformatics\/btr312","volume":"27","author":"K Wolstencroft","year":"2011","unstructured":"Wolstencroft K, Owen S, Horridge M, Krebs O, Mueller W, Snoep JL, du Preez F, Goble C. RightField: embedding ontology annotation in spreadsheets. Bioinformatics (Oxford, England). 2011; 27(14):2021\u20132. doi:10.1093\/bioinformatics\/btr312.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"Suplement1","key":"159_CR15","first-page":"55","volume":"13","author":"S Jupp","year":"2010","unstructured":"Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R. Populous: a tool for building OWL ontologies from templates. Semantic Web Appl Tools Life Sci. 2010; 13(Suplement1):55. doi:10.1186\/1471-2105-13-S1-S5.","journal-title":"Semantic Web Appl Tools Life Sci"},{"key":"159_CR16","doi-asserted-by":"crossref","unstructured":"Ega\u00f1a M, Stevens R, Antezana E. Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. Proc OWLED. 2009. doi:10.1038\/npre.2009.4006.1.","DOI":"10.1038\/npre.2009.4006.1"},{"issue":"Suppl 1","key":"159_CR17","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-13-S1-S5","volume":"13","author":"S Jupp","year":"2011","unstructured":"Jupp S, Horridge M, Iannone L, Klein J, Owen S, Schanstra J, Wolstencroft K, Stevens R. Populous: a tool for building owl ontologies from templates. BMC Bioinforma. 2011; 13(Suppl 1):S5. doi:10.1186\/1471-2105-13-S1-S5.","journal-title":"BMC Bioinforma"},{"key":"159_CR18","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1155\/2015\/471719","volume":"2015","author":"A Ten Brinke","year":"2015","unstructured":"Ten Brinke A, Hilkens CMU, Cools N, Geissler EK, Hutchinson JA, Lombardi G, Lord P, Sawitzki B, Trzonkowski P, Van Ham SM, et al.Clinical use of tolerogenic dendritic cells-harmonization approach in european collaborative effort. Mediat Inflamm. 2015; 2015:18. doi:10.1155\/2015\/471719.","journal-title":"Mediat Inflamm"},{"key":"159_CR19","unstructured":"Hilkens C. Cell Therapies: From the laboratory to the clinic. Cafe Sci Newcastle. 2016. https:\/\/www.youtube.com\/watch?v=Y1ESfJBxvqY. Accessed 27 June 2016."},{"issue":"1","key":"159_CR20","first-page":"11","volume":"2","author":"M Horridge","year":"2011","unstructured":"Horridge M, Bechhofer S. The owl api: A java api for owl ontologies. Semant Web. 2011; 2(1):11\u201321. http:\/\/dl.acm.org\/citation.cfm?id=2019470.2019471.","journal-title":"Semant Web"},{"key":"159_CR21","unstructured":"Horridge M, Patel-Schneider P. OWL 2 Web Ontology Language Manchester Syntax. 2012. http:\/\/www.w3.org\/TR\/owl2-manchester-syntax\/. Accessed 10 June 2016."},{"key":"159_CR22","unstructured":"Lord P. Manchester Syntax is a bit backward. 2014. http:\/\/www.russet.org.uk\/blog\/2985. Accessed 25 May 2016."},{"key":"159_CR23","unstructured":"Warrender JD, Lord P. How, what and why to test an ontology. CoRR. 2015. abs\/1505.04112."},{"key":"159_CR24","unstructured":"Warrender JD, Lord P. The karyotype ontology: a computational representation for human cytogenetic patterns. Bio-Ontologies. 2013. http:\/\/arxiv.org\/abs\/1305.3758."},{"key":"159_CR25","unstructured":"Warrender J, Lord P. Scaffolding the Mitochondrial Disease Ontology from Extant Knowledge Sources. 2015. 1505.04114. http:\/\/adsabs.harvard.edu\/abs\/2015arXiv150504114W. Accessed 11 June 2016."},{"key":"159_CR26","unstructured":"Stevens R, Sattler U. An object lesson in choosing between a class and an object. Ontogenesis. 2013. http:\/\/ontogenesis.knowledgeblog.org\/1418. Accessed 3 June 2016."},{"issue":"13","key":"159_CR27","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1093\/bioinformatics\/btn158","volume":"24","author":"S Schulz","year":"2008","unstructured":"Schulz S, Stenzhorn H, Boeker M. The ontology of biological taxa. Bioinformatics. 2008; 24(13):313\u201321. doi:10.1093\/bioinformatics\/btn158.","journal-title":"Bioinformatics"},{"key":"159_CR28","doi-asserted-by":"crossref","unstructured":"Lord P, Stevens R. Adding a little reality to building ontologies for biology. PLoS One. 2010. doi:10.1371\/journal.pone.0012258.","DOI":"10.1371\/journal.pone.0012258"},{"key":"159_CR29","unstructured":"Rector AL. Normalisation of ontology implementations: Towards modularity, re-use, and maintainability. In: Proceedings Workshop on Ontologies for Multiagent Systems (OMAS) inconjunction with European Knowledge Acquisition Workshop: 2002."},{"key":"159_CR30","unstructured":"Rector A. Representing Specified Values in OWL: \u201cvalue partitions\u201d and \u201cvalue sets\u201d: W3C Working Group Note; 2005. https:\/\/www.w3.org\/TR\/2005\/NOTE-swbp-specified-values-20050517\/. Accessed 11 May 2016."},{"key":"159_CR31","unstructured":"Noy N, Rector A. Defining N-ary Relations on the Semantic Web. W3C. 2006. https:\/\/www.w3.org\/TR\/swbp-n-aryRelations\/. Accessed 17 May 2016."},{"key":"159_CR32","volume-title":"PRISMATIC: Inducing Knowledge from a Large Scale Lexicalized Relation Resource. FAM-LbR \u201910","author":"J Fan","year":"2010","unstructured":"Fan J, Ferrucci D, Gondek D, Kalyanpur A. PRISMATIC: Inducing Knowledge from a Large Scale Lexicalized Relation Resource. FAM-LbR \u201910. Stroudsburg: Association for Computational Linguistics; 2010, pp. 122\u20137. http:\/\/dl.acm.org\/citation.cfm?id=1866775.1866790."},{"key":"159_CR33","unstructured":"Lord P. Ontology Connection Points. An Exerc Irrelevance. 2013. http:\/\/www.russet.org.uk\/blog\/2955. Accessed 11 Apr 2016."},{"key":"159_CR34","doi-asserted-by":"crossref","unstructured":"Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. MIREOT: the Minimum Information to Reference an External Ontology Term. Nat Precedings. 2009. http:\/\/precedings.nature.com\/documents\/3574\/version\/1. Accessed 21 July 2016.","DOI":"10.1038\/npre.2009.3576.1"},{"key":"159_CR35","unstructured":"Warrender J. The Consistent Representation of Scientific Knowledge: Investigations into the Ontology of Karyotypes and Mitochondria. 2015. https:\/\/theses.ncl.ac.uk\/dspace\/bitstream\/10443\/2910\/1\/Warrender%2c%20J%202015.pdf. Accessed 22 July 2015."},{"key":"159_CR36","unstructured":"Lord P, Warrender J. A highly literate approach to ontology building. 2015."},{"issue":"1","key":"159_CR37","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1186\/1471-2105-7-489","volume":"7","author":"TF Rayner","year":"2006","unstructured":"Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. A simple spreadsheet-based, miame-supportive format for microarray data: Mage-tab. BMC Bioinforma. 2006; 7(1):489. doi:10.1186\/1471-2105-7-489.","journal-title":"BMC Bioinforma"},{"key":"159_CR38","unstructured":"Johnson D, Gonzalez-Beltran A. ISA-tools. GitHub Repository. 2015. https:\/\/github.com\/ISA-tools\/isa-specs\/blob\/master\/source\/isatab.rst, Accessed 23 Feb 2017."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0159-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-017-0159-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0159-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:21:48Z","timestamp":1790036508000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13326-017-0159-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,28]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["159"],"URL":"https:\/\/doi.org\/10.1186\/s13326-017-0159-4","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,28]]},"assertion":[{"value":"13 February 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 November 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Newcastle University procedures determined that full ethical approval was not required for this research.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"The Authors consent to publish this Work in the thematic series Biomedical Ontologies (BIOONT series).","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","label":"Publisher\u2019s Note","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"54"}}