AlzPharm: integration of neurodegeneration data using RDF

BackgroundNeuroscientists 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.ResultsWe 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.ConclusionAccessing 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.

[1]  James J. Cimino,et al.  Using the UMLS to Bring the Library to the Bedside , 1991, Medical decision making : an international journal of the Society for Medical Decision Making.

[2]  Andy Seaborne,et al.  SWAN: A distributed knowledge infrastructure for Alzheimer disease research , 2006, J. Web Semant..

[3]  June Kinoshita,et al.  Alzheimer Research Forum live discussion: insulin resistance: a common axis linking Alzheimer's, depression, and metabolism? , 2006, Journal of Alzheimer's disease : JAD.

[4]  Wendy Hall,et al.  Creating a Science of the Web , 2006, Science.

[5]  Mark Ellisman,et al.  e-Neuroscience: challenges and triumphs in integrating distributed data from molecules to brains , 2004, Nature Neuroscience.

[6]  Anne E. Trefethen,et al.  Cyberinfrastructure for e-Science , 2005, Science.

[7]  M. F. Huerta,et al.  The human brain project: an international resource , 1993, Trends in Neurosciences.

[8]  Bonnie L. Webber,et al.  COBrA: a bio-ontology editor , 2005, Bioinform..

[9]  Frank van Harmelen,et al.  Web Ontology Language: OWL , 2004, Handbook on Ontologies.

[10]  Mary K Pulvermacher,et al.  Toward the Use of an Upper Ontology for U.S. Government and U.S. Military Domains: An Evaluation , 2004 .

[11]  Stephen Stead,et al.  Uniform Resource Identifier , 2020, Encyclopedia of Database Systems.

[12]  Susie Stephens,et al.  Applying semantic Web technologies to drug safety determination , 2006, IEEE Intelligent Systems.

[13]  Robert Hoehndorf,et al.  A top-level ontology of functions and its application in the Open Biomedical Ontologies , 2006, ISMB.

[14]  Jeff Z. Pan,et al.  Resource Description Framework , 2020, Definitions.

[15]  S. Koslow,et al.  Discovery and Integrative Neuroscience , 2005, Clinical EEG and neuroscience.

[16]  BMC Bioinformatics , 2005 .

[17]  Diego Calvanese,et al.  The Description Logic Handbook , 2007 .

[18]  L. Stein,et al.  Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages , 2005, Comparative and functional genomics.

[19]  Huajun Chen,et al.  RDF/RDFS-based Relational Database Integration , 2006, 22nd International Conference on Data Engineering (ICDE'06).

[20]  Thomas R. Gruber,et al.  A translation approach to portable ontology specifications , 1993, Knowl. Acquis..

[21]  Perry L. Miller,et al.  Application of Information Technology: Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances , 2003, J. Am. Medical Informatics Assoc..

[22]  Volker Haarslev,et al.  Querying the Semantic Web with Racer + nRQL , 2004 .

[23]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.