AlzPharm: integration of neurodegeneration data using RDF

BMC Bioinformatics - Tập 8 - Trang 1-12 - 2007
Hugo YK Lam1, Luis Marenco2,3, Tim Clark4,5, Yong Gao5, June Kinoshita6, Gordon Shepherd7, Perry Miller2,3,8, Elizabeth Wu6, Gwendolyn T Wong6, Nian Liu2,3, Chiquito Crasto2,7, Thomas Morse7, Susie Stephens9, Kei-Hoi Cheung2,3,10,11
1Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
2Center for Medical Informatics, Yale University, New Haven, USA
3Department of Anesthesiology, Yale University, New Haven, USA
4Initiative in Innovative Computing, Harvard University, Cambridge, USA
5Massachusetts General Hospital, Boston, USA
6Alzheimer Research Forum, USA
7Department of Neurobiology, Yale University, New Haven, USA
8Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, USA
9Oracle, Burlington, USA
10Department of Genetics, Yale University, New Haven, USA
11Department of Computer Science, Yale University, New Haven, USA

Tóm tắt

Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.

Tài liệu tham khảo

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BMC Bioinformatics

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