title: Mapping proteins to disease terminologies: from UniProt to MeSH.
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.
authors.affiliation: Swiss-Prot Group, Swiss Institute of Bioinformatics, 1211 Genève 4, Switzerland. anais.mottaz@isb-sib.ch
authors.forename: Anaïs
authors.initials: A
authors.lastname: Mottaz
authors.forename: Yum L
authors.initials: YL
authors.lastname: Yip
authors.forename: Patrick
authors.initials: P
authors.lastname: Ruch
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Veuthey
mesh_terms: D035843:Biomedical Research / Q000379:methods / Q000458:organization & administration; D030562:Databases, Protein; D004194:Disease; D006801:Humans; D051188:Knowledge Bases; D046650:Medical Subject Headings; D040901:Proteomics / Q000379:methods; D012660:Semantics; D018511:Systems Integration; D009626:Terminology as Topic