UNIGE document Scientific Article
previous document  unige:2727  next document
add to browser collection

Mapping proteins to disease terminologies: from UniProt to MeSH

Published in BMC bioinformatics. 2008, vol. 9, no. Suppl 5, S3
Abstract BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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: http://research.isb-sib.ch/unimed.
Keywords Biomedical Research/methods/organization & administrationDatabases, ProteinDiseaseHumansKnowledge BasesMedical Subject HeadingsProteomics/methodsSemanticsSystems IntegrationTerminology as Topic
PMID: 18460185
Full text
Research group CALIPHO (80)
(ISO format)
MOTTAZ, Anais et al. Mapping proteins to disease terminologies: from UniProt to MeSH. In: BMC Bioinformatics, 2008, vol. 9, n° Suppl 5, p. S3. doi: 10.1186/1471-2105-9-S5-S3 https://archive-ouverte.unige.ch/unige:2727

548 hits



Deposited on : 2009-09-21

Export document
Format :
Citation style :