City Research Online

Logic-based assessment of the compatibility of UMLS ontology sources.

Jimenez-Ruiz, E. ORCID: 0000-0002-9083-4599, Grau, B. C., Horrocks, I. & Berlanga, R. (2011). Logic-based assessment of the compatibility of UMLS ontology sources.. Journal of Biomedical Semantics, 2(Suppl ), article number S2. doi: 10.1186/2041-1480-2-s1-s2


BACKGROUND: The UMLS Metathesaurus (UMLS-Meta) is currently the most comprehensive effort for integrating independently-developed medical thesauri and ontologies. UMLS-Meta is being used in many applications, including PubMed and The integration of new sources combines automatic techniques, expert assessment, and auditing protocols. The automatic techniques currently in use, however, are mostly based on lexical algorithms and often disregard the semantics of the sources being integrated.

RESULTS: In this paper, we argue that UMLS-Meta's current design and auditing methodologies could be significantly enhanced by taking into account the logic-based semantics of the ontology sources. We provide empirical evidence suggesting that UMLS-Meta in its 2009AA version contains a significant number of errors; these errors become immediately apparent if the rich semantics of the ontology sources is taken into account, manifesting themselves as unintended logical consequences that follow from the ontology sources together with the information in UMLS-Meta. We then propose general principles and specific logic-based techniques to effectively detect and repair such errors.

CONCLUSIONS: Our results suggest that the methodologies employed in the design of UMLS-Meta are not only very costly in terms of human effort, but also error-prone. The techniques presented here can be useful for both reducing human effort in the design and maintenance of UMLS-Meta and improving the quality of its contents.

Publication Type: Article
Additional Information: © 2011 Jiménez-Ruiz et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the CreativeCommons Attribution License (, which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
R Medicine
Departments: School of Science & Technology > Computer Science
SWORD Depositor:
[thumbnail of Logic-based assessment of the compatibility of UMLS ontology sources.pdf]
Text - Accepted Version
Available under License Creative Commons Attribution.

Download (1MB) | Preview


Add to AnyAdd to TwitterAdd to FacebookAdd to LinkedinAdd to PinterestAdd to Email


Downloads per month over past year

View more statistics

Actions (login required)

Admin Login Admin Login