Abstract
We present a method for creating mappings between the Orphanet terminology of rare diseases and the Unified Medical Language System (UMLS), in particular the SNOMED CT, MeSH, and MedDRA terminologies. Our method is based on: (i) aggressive normalisation of terms specific to the Orphanet terminology on top of standard UMLS normalisation; (ii) semantic ranking of partial candidate mappings in order to group similar mappings and attribute higher ranking to the more informative ones. Our results show that, by using the aggressive normalisation function, we increase the number of exact candidate mappings by 7.1-9.5% compared to a mapping method based on MetaMap. A manual assessment of our results shows a high precision of 94.6%. Our results imply that Orphanet diseases are under-represented in the aforementioned terminologies: SNOMED CT, MeSH, and MedDRA are found to contain only 35%, 42%, and 15% of the Orphanet rare diseases, respectively.
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References
Aronson, A.: Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program. In: AMIA 2001 Symposium Proc. (2001)
Ayme, S., Urbero, B., Oziel, D., Lecouturier, E., Biscarat, A.: Information on rare diseases: the Orphanet project. Rev. Med. Interne. 19 Suppl 3, 376–377 (1998)
Bechhofer, S., van Hamerlen, F., Hendler, J., Horrocks, I., McGuinness, D.L., Patel-Schneider, P., Stein, L.: OWL Web Ontology Language reference. W3C Recommendation (2004), http://www.w3.org/TR/owl-ref/
Ghazvinian, A., Noy, N., Musen, M.: Creating Mappings For Ontologies in Biomedicine: Simple Methods Work. In: AMIA 2009 Symposium Proc. (2009)
Merabti, T., Joubert, M., Lecroq, T., Rath, A., Darmoni, S.: Mapping biomedical terminologies using natural language processing tools and UMLS: Mapping the Orphanet thesaurus to the MeSH. IRBM 31(4), 221–225 (2010)
Merabti, T.: Methods to map health terminologies: contribution to the semantic interoperability between health terminologies. PhD thesis, University of Rouen (2010)
Pasceri, E., Rance, B., Rath, A., Lewis, J., Snyder, M., Bodenreider, O.: Representation of Rare Diseases in Biomedical Terminologies (submitted)
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© 2011 Springer-Verlag Berlin Heidelberg
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Miličić Brandt, M., Rath, A., Devereau, A., Aymé, S. (2011). Mapping Orphanet Terminology to UMLS. In: Peleg, M., Lavrač, N., Combi, C. (eds) Artificial Intelligence in Medicine. AIME 2011. Lecture Notes in Computer Science(), vol 6747. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22218-4_24
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DOI: https://doi.org/10.1007/978-3-642-22218-4_24
Publisher Name: Springer, Berlin, Heidelberg
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