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

Jiménez-Ruiz E, Grau BC, Horrocks I, Berlanga R - J Biomed Semantics (2011)

Bottom Line: We then propose general principles and specific logic-based techniques to effectively detect and repair such errors.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Lenguajes y Sistemas Informáticos, Universitat Jaume I, Campus de Riu Sec, Castellón, Spain. ernesto.jimenez.ruiz@gmail.com.

ABSTRACT

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 ClinicalTrials.gov. 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.

No MeSH data available.


Consistency principle violation between FMA and NCI mappings
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3105494&req=5

Figure 2: Consistency principle violation between FMA and NCI mappings

Mentions: For example, as shown in Figure 2, UMLS-Meta maps the FMA concept Protein to the NCI concept Protein, and the FMA concept Lymphokine to the NCI concept Therapeutic_Lymphokine. In FMA, Lymphokine is a Protein, whereas in NCI Therapeutίc_Lίmphokίne is a Pharmacologic_Substance. Furthermore, Pharmacologic_Substance and Protein are disjoint in NCI and hence the union of NCI, FMA and UMLS-Meta would imply that Lymphokine and Therapeutic_Limphokine are unsatisfiable (i.e.,there can be no instances of either entity).


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

Jiménez-Ruiz E, Grau BC, Horrocks I, Berlanga R - J Biomed Semantics (2011)

Consistency principle violation between FMA and NCI mappings
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105494&req=5

Figure 2: Consistency principle violation between FMA and NCI mappings
Mentions: For example, as shown in Figure 2, UMLS-Meta maps the FMA concept Protein to the NCI concept Protein, and the FMA concept Lymphokine to the NCI concept Therapeutic_Lymphokine. In FMA, Lymphokine is a Protein, whereas in NCI Therapeutίc_Lίmphokίne is a Pharmacologic_Substance. Furthermore, Pharmacologic_Substance and Protein are disjoint in NCI and hence the union of NCI, FMA and UMLS-Meta would imply that Lymphokine and Therapeutic_Limphokine are unsatisfiable (i.e.,there can be no instances of either entity).

Bottom Line: We then propose general principles and specific logic-based techniques to effectively detect and repair such errors.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Lenguajes y Sistemas Informáticos, Universitat Jaume I, Campus de Riu Sec, Castellón, Spain. ernesto.jimenez.ruiz@gmail.com.

ABSTRACT

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 ClinicalTrials.gov. 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.

No MeSH data available.