{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T01:03:38Z","timestamp":1790039018500,"version":"4.0.1"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T00:00:00Z","timestamp":1492992000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T00:00:00Z","timestamp":1492992000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"National Library Of Medicine of the National Institutes of Health","award":["R01LM011829"],"award-info":[{"award-number":["R01LM011829"]}]},{"name":"Cancer Prevention Research Institute of Texas (CPRIT) Training Grant","award":["RP160015"],"award-info":[{"award-number":["RP160015"]}]}],"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>Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, specifically towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using the semiotic-based evaluation framework for drug-based ontologies, we adjusted the quality metrics based on the semiotic features of drug ontologies. Then, we compared the quality scores before and after tailoring. The scores revealed a more precise measurement and a closer distribution compared to the before-tailoring.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The results of this study reveal that a tailored semiotic evaluation produced a more meaningful and accurate assessment of drug-based ontologies, lending to the possible usefulness of semiotics in ontology evaluation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-017-0124-2","type":"journal-article","created":{"date-parts":[[2017,4,24]],"date-time":"2017-04-24T08:24:44Z","timestamp":1493022284000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Modulated evaluation metrics for drug-based ontologies"],"prefix":"10.1186","volume":"8","author":[{"given":"Muhammad","family":"Amith","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cui","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,4,24]]},"reference":[{"key":"124_CR1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25\u20139.","journal-title":"Nat Genet"},{"key":"124_CR2","doi-asserted-by":"publisher","first-page":"D267","DOI":"10.1093\/nar\/gkh061","volume":"32","author":"O Bodenreider","year":"2004","unstructured":"Bodenreider O. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004; 32:D267\u201370.","journal-title":"Nucleic Acids Res"},{"key":"124_CR3","unstructured":"Spackman KA, Campbell KE, C\u00f4t\u00e9 RA. SNOMED RT: a reference terminology for health care. In: Proceedings of the AMIA annual fall symposium: 1997. p. 640\u20134. https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2233423\/, https:\/\/www.ncbi.nlm.nih.gov\/pmc\/issues\/160771\/."},{"key":"124_CR4","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; 25:1251\u20135.","journal-title":"Nat Biotechnol"},{"key":"124_CR5","unstructured":"Merriam-Webster. Semiotics. Merriam-Webster. 2016. [cited 2015 Nov 1]. Available from: https:\/\/www.merriam-webster.com\/dictionary\/semiotics. Accessed 10 Apr 2017."},{"key":"124_CR6","doi-asserted-by":"crossref","unstructured":"Sowa JF. Ontology, metadata, and semiotics. Conceptual structures: Logical, linguistic, and computational issues: Springer; 2000, pp. 55\u201381. http:\/\/link.springer.com\/chapter\/10.1007\/10722280_5. Accessed 10 Apr 2017.","DOI":"10.1007\/10722280_5"},{"key":"124_CR7","doi-asserted-by":"crossref","unstructured":"Brewster C, Alani H, Dasmahapatra S, Wilks Y. Data driven ontology evaluation. The 4th International Conference on Language Resources and Evaluation: Lisbon; 2004. http:\/\/oro.open.ac.uk\/20045\/. Accessed 10 Apr 2017.","DOI":"10.63317\/4f6s9jyb29f4"},{"key":"124_CR8","unstructured":"Alani H, Brewster C. Metrics for ranking ontologies. In: Proceedings of 4th International EON Workshop: 2006. http:\/\/eprints.ecs.soton.ac.uk\/12603. Accessed 10 Apr 2017."},{"key":"124_CR9","unstructured":"Brank J, Grobelnik M, Mladeni\u0107 D. A survey of ontology evaluation techniques. In: Proceedings of the conference on data mining and data warehouses (SiKDD 2005): 2005. p. 166\u201370. http:\/\/ailab.ijs.si\/dunja\/sikdd2005\/papers\/BrankEvaluationSiKDD2005.pdf. Accessed 10 Apr 2017."},{"key":"124_CR10","doi-asserted-by":"crossref","unstructured":"Dellschaft K, Staab S. On how to perform a gold standard based evaluation of ontology learning. The Semantic Web-ISWC 2006: Springer; 2006, pp. 228\u2013241. http:\/\/link.springer.com\/chapter\/10.1007\/11926078_17. Accessed 10 Apr 2017.","DOI":"10.1007\/11926078_17"},{"key":"124_CR11","volume-title":"International Conference on Information and Knowledge Engineering","author":"V Parekh","year":"2004","unstructured":"Parekh V, Gwo J, Finin TW. Mining Domain Specific Texts and Glossaries to Evaluate and Enrich Domain Ontologies. In: International Conference on Information and Knowledge Engineering. Las Vegas: CSREA Press: 2004. p. 533\u201340. ISBN:1-932415-27-0."},{"key":"124_CR12","volume-title":"International Semantic Web Conference","author":"J V\u00f6lker","year":"2005","unstructured":"V\u00f6lker J, Vrand\u011bci\u0107 D, Sure Y. Automatic evaluation of ontologies (AEON). In: International Semantic Web Conference. Berlin: Springer: 2005. p. 716\u201331."},{"key":"124_CR13","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.datak.2004.11.010","volume":"55","author":"A Burton-Jones","year":"2005","unstructured":"Burton-Jones A, Storey VC, Sugumaran V, Ahluwalia P. A semiotic metrics suite for assessing the quality of ontologies. Data Knowl Eng. 2005; 55:84\u2013102.","journal-title":"Data Knowl Eng"},{"key":"124_CR14","unstructured":"RxNORM. National Center for Biomedical Ontology BioPortal. 2015. http:\/\/bioportal.bioontology.org\/ontologies\/RXNORM. Accessed 10 Apr 2017."},{"key":"124_CR15","unstructured":"Veterans Health Administration National Drug File. National Center for Biomedical Ontology BioPortal. 2015. http:\/\/bioportal.bioontology.org\/ontologies\/VANDF. Accessed 10 Apr 2017."},{"key":"124_CR16","unstructured":"The Drug Ontology. National Center for Biomedical Ontology BioPortal. 2015. http:\/\/bioportal.bioontology.org\/ontologies\/DRON. Accessed 10 Apr 2017."},{"key":"124_CR17","unstructured":"The Drug-Drug Interactions Ontology. National Center for Biomedical Ontology BioPortal. 2016. http:\/\/bioportal.bioontology.org\/ontologies\/DINTO. Accessed 10 Apr 2017."},{"key":"124_CR18","unstructured":"Drug Interaction Knowledge Base Ontology. National Center for Biomedical Ontology BioPortal. 2015. http:\/\/bioportal.bioontology.org\/ontologies\/DIKB. Accessed 10 Apr 2017."},{"key":"124_CR19","unstructured":"Vaccine Ontology. National Center for Biomedical Ontology BioPortal. 2016. http:\/\/bioportal.bioontology.org\/ontologies\/VO. Accessed 10 Apr 2017."},{"key":"124_CR20","unstructured":"Pharmacovigilance Ontology. National Center for Biomedical Ontology Bioportal. 2011. http:\/\/bioportal.bioontology.org\/ontologies\/PVONTO. Accessed 10 Apr 2017."},{"key":"124_CR21","unstructured":"OWL API. 2016. http:\/\/owlapi.sourceforge.net\/. Accessed 10 Apr 2017."},{"key":"124_CR22","unstructured":"JWI (the MIT Java Wordnet Interface). 2016. http:\/\/projects.csail.mit.edu\/jwi\/. Accessed 10 Apr 2017."},{"key":"124_CR23","unstructured":"Apache Commons Lang. 2015. https:\/\/commons.apache.org\/proper\/commons-lang\/. Accessed 10 Apr 2017."},{"key":"124_CR24","unstructured":"Minimal-Json. 2016. https:\/\/github.com\/ralfstx\/minimal-json. Accessed 10 Apr 2017."},{"key":"124_CR25","volume-title":"Genetic programming: on the programming of computers by means of natural selection","author":"JR Koza","year":"1992","unstructured":"Koza JR. Genetic programming: on the programming of computers by means of natural selection. Cambridge: Mass: MIT press; 1992."},{"key":"124_CR26","unstructured":"Amith M, Tao C. A Web Application Towards Semiotic-based Evaluation of Biomedical Ontologies. Proceedings of International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration: A Promising Approach to Solving Unmet Medical Needs (BDM2I 2015); 2015. Available from http:\/\/ceur-ws.org\/Vol-1428\/BDM2I_2015_paper_5.pdf. Accessed 10 Apr 2017."}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0124-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-017-0124-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-017-0124-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:20:55Z","timestamp":1790036455000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13326-017-0124-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,4,24]]},"references-count":26,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,12]]}},"alternative-id":["124"],"URL":"https:\/\/doi.org\/10.1186\/s13326-017-0124-2","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,4,24]]},"assertion":[{"value":"22 November 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 March 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"17"}}