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This article is part of the supplement: Proceedings of the 10th Bio-Ontologies Special Interest Group Workshop 2007. Ten years past and looking to the future

Open Access Proceedings

Mapping proteins to disease terminologies: from UniProt to MeSH

Anaïs Mottaz1, Yum L Yip12, Patrick Ruch3 and Anne-Lise Veuthey1*

Author Affiliations

1 Swiss-Prot Group, Swiss Institute of Bioinformatics, 1211 Genève 4, Switzerland

2 Department of Structural Biology and Bioinformatics, University of Geneva, 1211 Genève 4, Switzerland

3 Medical Informatics Service, Hôpitaux Universitaire de Genève, 1211 Genève 4, Switzerland

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BMC Bioinformatics 2008, 9(Suppl 5):S3  doi:10.1186/1471-2105-9-S5-S3

Published: 29 April 2008



Although the UniProt KnowledgeBase is not a medical-oriented database, it contains information on more than 2,000 human proteins involved in pathologies. However, these annotations are not standardized, which impairs the interoperability between biological and clinical resources. In order to make these data easily accessible to clinical researchers, we have developed a procedure to link diseases described in the UniProtKB/Swiss-Prot entries to the MeSH disease terminology.


We mapped disease names extracted either from the UniProtKB/Swiss-Prot entry comment lines or from the corresponding OMIM entry to the MeSH. Different methods were assessed on a benchmark set of 200 disease names manually mapped to MeSH terms. The performance of the retained procedure in term of precision and recall was 86% and 64% respectively. Using the same procedure, more than 3,000 disease names in Swiss-Prot were mapped to MeSH with comparable efficiency.


This study is a first attempt to link proteins in UniProtKB to the medical resources. The indexing we provided will help clinicians and researchers navigate from diseases to genes and from genes to diseases in an efficient way. The mapping is available at: webcite.