title: A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.
abstract: In the Semantic Enrichment of the Scientific Literature (SESL) project, researchers from academia and from life science and publishing companies collaborated in a pre-competitive way to integrate and share information for type 2 diabetes mellitus (T2DM) in adults. This case study exposes benefits from semantic interoperability after integrating the scientific literature with biomedical data resources, such as UniProt Knowledgebase (UniProtKB) and the Gene Expression Atlas (GXA). We annotated scientific documents in a standardized way, by applying public terminological resources for diseases and proteins, and other text-mining approaches. Eventually, we compared the genetic causes of T2DM across the data resources to demonstrate the benefits from the SESL triple store. Our solution enables publishers to distribute their content with little overhead into remote data infrastructures, such as into any Virtual Knowledge Broker.
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Computerlinguistik, Universität Zürich, Binzmühlestrasse 14, 8050 Zürich, Switzerland. Electronic address: rebholz@ebi.ac.uk.
authors.forename: Dietrich
authors.initials: D
authors.lastname: Rebholz-Schuhmann
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Christoph
authors.initials: C
authors.lastname: Grabmüller
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Silvestras
authors.initials: S
authors.lastname: Kavaliauskas
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Samuel
authors.initials: S
authors.lastname: Croset
authors.affiliation: GlaxoSmithKline, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Woollard
authors.affiliation: Albert-Ludwigs-University Freiburg, Fahnenbergplatz, D-79085 Freiburg, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.affiliation: Unilever R&D, Colworth Science Park, Sharnbrook MK44 1LQ, UK.
authors.forename: Wendy
authors.initials: W
authors.lastname: Filsell
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Dominic
authors.initials: D
authors.lastname: Clark
mesh_terms: D000818:Animals; D035843:Biomedical Research / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D003924:Diabetes Mellitus, Type 2 / Q000175:diagnosis / Q000235:genetics*; D006801:Humans; D051188:Knowledge Bases; D012660:Semantics; D018511:Systems Integration