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

Hey T, Trefethen AE: Cyberinfrastructure for e-Science. Science 2005, 308(5723):817–21. 10.1126/science.1110410 Martone ME, Gupta A, Ellisman MH: E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 2004, 7(5):467–472. 10.1038/nn1229 Huerta MF, Koslow SH, Leshner AI: The Human Brain Project: an international resource. Trends Neurosci 1993, 16(11):436–8. 10.1016/0166-2236(93)90069-X Koslow SH: Discovery and integrative neuroscience. Clin EEG Neurosci 2005, 36(2):55–63. Neuroscience Database Gateway[http://big.sfn.org/NDG/site/] Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S, Ellisman MH: The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 2003, 1(4):379–96. 10.1385/NI:1:4:379 Marenco L, Tosches N, Crasto C, Shepherd G, Miller PL, Nadkarni PM: Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances. J Am Med Inform Assoc 2003, 10(5):444–453. 10.1197/jamia.M1303 Gruber T: Ontolingua: a translation approach to providing portable ontology specifications. Knowledge Acquisition 1993, 5(2):199–200. 10.1006/knac.1993.1008 Semy SK, Pulvermacher MK, Obrst LJ: Toward the Use of an Upper Ontology for U.S. Government and U.S. Military Domains. Mitre technical report: MTR-04B0000063 2004. Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry M, Davis A, Dolinski K, Dwight S, Eppig J, et al.: Gene ontology: tool for the unification of biology. Nature Genetics 2000, 25: 25–29. 10.1038/75556 Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, et al.: Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics 2005, 6: 388–97. 10.1002/cfg.496 Cimino J, Sideli R: Using the UMLS to bring the library to the bedside. Med Decis Making 1991, 11(4 Suppl):S116–20. National Center for Biomedical Ontologies[http://www.bioontology.org] Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H, Kelso J: A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics 2006, 22(14):e66-e73. 10.1093/bioinformatics/btl266 Functional Geneomics Investigation Ontology[http://fugo.sourceforge.net/] Ontology of Experiment[http://expo.sourceforge.net/] Resource Description Framework[http://www.w3.org/RDF/] Web Ontology Language (OWL)[http://www.w3.org/TR/owl-features/] RDF Schema[http://www.w3.org/TR/rdf-schema/] Uniform Resource Identifier[http://www.w3.org/Addressing/] Baader F, Calvanese D, McGuinness D, Nardi D, Patel-Schneider P: The Description Logic Handbook. Cambridge University Press; 2002. Protege[http://protege.stanford.edu/] WebOnto[http://kmi.open.ac.uk/projects/webonto/] GrOWL[http://ecoinformatics.uvm.edu/technologies/growl-knowledge-modeler.html] Aitken S, Korf R, Webber B, Bard J: COBrA: a bio-ontology editor. Bioinformatics 2005, 21(6):825–6. 10.1093/bioinformatics/bti097 PerlRDF[http://www.gingerall.org/perlrdf.html] Jena[http://jena.sourceforge.net/] Sesame[http://www.openrdf.org/] Kowari[http://kowari.sourceforge.net/] Oracle RDF Data Model[http://www.oracle.com/technology/tech/semantic_technologies] SPARQL[http://www.w3.org/TR/rdf-sparql-query] D2RQ[http://sites.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/] Haarslev V, Moeller R, Wessel M: Querying the Semantic Web with Racer + nRQL. In Proceedings of the KI-04 Workshop on Applications of Description Logics. Ulm, Germany: Deutsche Bibliothek; 2004. FaCT[http://www.ontoknowledge.org/tools/fact.shtml] Pellet[http://www.mindswap.org/2003/pellet/] Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T: SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research. Journal of Web Semantics 2006., 4(3): AlzPharm[http://ontoweb.med.yale.edu/AlzPharm] Kinoshita J, Fagan A, Ewbank D, Marlatt M, Heyn P, Monte Sdl, Lombardo NE: Alzheimer Research Forum live discussion: insulin resistance: a common axis linking Alzheimer's, depression, and metabolism? Journal of Alzheimer's Disease 2006, 9(1):89–93. Berners-Lee T, Hall W, Hendler J, Shadbolt N, Weitzner DJ: Creating a Science of the Web. Science 2006, 313: 769–771. 10.1126/science.1126902 Chen H, Wu Z, Wang H, Mao Y: RDF/RDFS-based Relational Database Integration. ICDE. Atlanta, Georgia 2006, 94. Stephens S, Morales A, Quinian M: Applying semantic web technologies to drug safety determination. IEEE Intelligent Systems 2006, 21(1):82–6. 10.1109/MIS.2006.2 BrainPharm[http://senselab.med.yale.edu/BrainPharm] Semantic Web Applications in Neuromedicine[http://swan.mindinformatics.org] Alzheimer Research Forum[http://www.alzforum.org]