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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.


Conservativity principle violation between FMA and SNOMED CT mappings
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Figure 1: Conservativity principle violation between FMA and SNOMED CT mappings

Mentions: The conservativity principle is based on the purpose of M, which is to enable the interaction between O1 and O2, rather than to provide a new description of the domain. In the case of our previous example about “Joints”, UMLS-Meta contains two mappings establishing the equivalence between the entity Joint_structure from SNOMED CT and the FMA entities Joint and Set_of_joints respectively. As a consequence, UMLS-Meta implies that Joint is also equivalent to Set_of_joints. However, in FMA Joint neither subsumes, nor it is subsumed by Set_of_joints (see Figure 1). The conservativity principle suggests that the obtained mappings are in conflict and (at least) one of them is likely to be incorrect.


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

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

Conservativity principle violation between FMA and SNOMED CT mappings
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Conservativity principle violation between FMA and SNOMED CT mappings
Mentions: The conservativity principle is based on the purpose of M, which is to enable the interaction between O1 and O2, rather than to provide a new description of the domain. In the case of our previous example about “Joints”, UMLS-Meta contains two mappings establishing the equivalence between the entity Joint_structure from SNOMED CT and the FMA entities Joint and Set_of_joints respectively. As a consequence, UMLS-Meta implies that Joint is also equivalent to Set_of_joints. However, in FMA Joint neither subsumes, nor it is subsumed by Set_of_joints (see Figure 1). The conservativity principle suggests that the obtained mappings are in conflict and (at least) one of them is likely to be incorrect.

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.