title: AlzPharm: integration of neurodegeneration data using RDF.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. Hugo.YK.Lam@yale.edu <Hugo.YK.Lam@yale.edu>
authors.forename: Hugo Y K
authors.initials: HY
authors.lastname: Lam
authors.forename: Luis
authors.initials: L
authors.lastname: Marenco
authors.forename: Tim
authors.initials: T
authors.lastname: Clark
authors.forename: Yong
authors.initials: Y
authors.lastname: Gao
authors.forename: June
authors.initials: J
authors.lastname: Kinoshita
authors.forename: Gordon
authors.initials: G
authors.lastname: Shepherd
authors.forename: Perry
authors.initials: P
authors.lastname: Miller
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Wu
authors.forename: Gwendolyn T
authors.initials: GT
authors.lastname: Wong
authors.forename: Nian
authors.initials: N
authors.lastname: Liu
authors.forename: Chiquito
authors.initials: C
authors.lastname: Crasto
authors.forename: Thomas
authors.initials: T
authors.lastname: Morse
authors.forename: Susie
authors.initials: S
authors.lastname: Stephens
authors.forename: Kei-Hoi
authors.initials: KH
authors.lastname: Cheung
mesh_terms: D001921:Brain / Q000378:metabolism*; D003628:Database Management Systems; D016208:Databases, Factual; D004282:Documentation / Q000379:methods; D006801:Humans; D033181:Information Dissemination / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D038622:Internationality; D020407:Internet; D009323:Natural Language Processing; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D019636:Neurodegenerative Diseases / Q000145:classification / Q000378:metabolism*; D009488:Neurosciences / Q000379:methods / Q000458:organization & administration; D010865:Pilot Projects; D012106:Research / Q000458:organization & administration; D012107:Research Design; D012660:Semantics; D018511:Systems Integration
chemical_list: D009419:Nerve Tissue Proteins