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This article is part of the supplement: Second International Symposium on Semantic Mining in Biomedicine (SMBM)

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Mapping data elements to terminological resources for integrating biomedical data sources

Fleur Mougin1*, Anita Burgun1 and Olivier Bodenreider2

Author Affiliations

1 EA 3888, IFR 140, Faculté de Médecine, Université de Rennes I, France

2 National Library of Medicine, Bethesda, Maryland, USA

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BMC Bioinformatics 2006, 7(Suppl 3):S6  doi:10.1186/1471-2105-7-S3-S6

Published: 24 November 2006



Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration.


We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings.


82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed.


Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.