Artificial Intelligence in Medicine
Volume 48, Issue 1 , Pages 21-28 , January 2010

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience

  • Matthias Samwald

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
    • Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland
    • Konrad Lorenz Institute for Evolution and Cognition Research, Adolf Lorenz Gasse 2, A-3422 Altenberg, Austria
    • Section on Medical Expert and Knowledge-Based Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
    • Corresponding Author InformationCorresponding author at: Konrad Lorenz Institute for Evolution and Cognition Research, Adolf Lorenz Gasse 2, A-3422 Altenberg, Austria. Tel.: +43 2242 32390x19; fax: +43 2242 323904.
  • ,
  • Huajun Chen

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
    • College of Computer Science, Zhejiang University, 310027 Hangzhou, China
  • ,
  • Alan Ruttenberg

      Affiliations

    • Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, MA 02139, USA
  • ,
  • Ernest Lim

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
  • ,
  • Luis Marenco

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
    • Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
  • ,
  • Perry Miller

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
    • Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
    • Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8009, USA
  • ,
  • Gordon Shepherd

      Affiliations

    • Department of Neurobiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
  • ,
  • Kei-Hoi Cheung

      Affiliations

    • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
    • Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
    • Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005, USA
    • Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA

Received 24 August 2007 ,Revised 6 October 2009 ,Accepted 16 November 2009.

References 

  1. Martone ME, Gupta A, Ellisman MH. E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nature Neuroscience. 2004;7(5):467–472
  2. http://www.w3.org/ [accessed 15.01.09].
  3. http://www.w3.org/RDF/ [accessed 15.01.09].
  4. http://www.w3.org/TR/owl-features/ [accessed 15.01.09].
  5. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, et al. Advancing translational research with the Semantic Web. BMC Bioinformatics. 2006;8(Suppl. 3):S2
  6. http://esw.w3.org/topic/HCLS/Banff2007Demo [accessed 15.01.09].
  7. Samwald M, Bug W, Rees J, Mungall C, Barkley J, Hookway R, et al. The Semantic Web Health Care and Life Sciences Interest Group work in progress: a large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies. Poster Bio-Ontologies Special Interest Group workshop at the international conference on intelligent systems for molecular biology; 2007.
  8. Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, et al. SenseLab: new developments in disseminating neuroscience information. Briefings in Bioinformatics. 2007;8(3):150–162
  9. Liu N, Marenco L, Miller PL. ResourceLog: an embeddable tool for dynamically monitoring the usage of web-based bioscience resources. Journal of the American Medical Informatics Association. 2006;13(4):432–437
  10. Marenco L, Tosches N, Crasto C, Shepherd G, Millera PL, Nadkarni PM. Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances. Journal of the American Medical Informatics Association. 2003;10(5):444–453
  11. Smith B. Beyond concepts: ontology as reality representation. In:  Varzi A,  Vieu L editor. Proceedings of the international conference on formal ontology in information systems. Amsterdam: IOS Press; 2004;p. 319–330
  12. http://obofoundry.org/ [accessed 15.01.09].
  13. http://protege.stanford.edu [accessed 15.01.09].
  14. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y. Pellet: a practical OWL-DL reasoner. Web Semantics: Science, Services and Agents on the World Wide Web. 2007;5(2):51–53
  15. http://www.mindswap.org/2004/SWOOP/ [accessed 15.01.09].
  16. http://www.topbraidcomposer.com [accessed 15.01.09].
  17. Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, et al. Relations in biomedical ontologies. Genome Biology. 2005;6(5):R46
  18. http://www.obofoundry.org/ro/ [accessed 15.01.09].
  19. http://www.obofoundry.org/ [accessed 15.01.09].
  20. http://www.ifomis.uni-saarland.de/bfo [accessed 15.01.09].
  21. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 2007;25:1251–1255
  22. 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. Journal of the American Medical Informatics Association. 2003;10(5):444–453
  23. http://bioinformatics.ubc.ca/atlas/downloads/ [accessed 15.01.09].
  24. http://idconverter.bioinfo.cnio.es/ [accessed 15.01.09].
  25. http://smd.stanford.edu/cgi-bin/source/sourceBatchSearch [accessed 15.01.09].
  26. http://sw.neurocommons.org/2007/uri-explanation.html [accessed 15.01.09].
  27. Bota M, Dong H, Swanson LW. Brain architecture management system. Neuroinformatics. 2005;3(1):15–48
  28. http://brancusi.usc.edu/bkms/ [accessed 15.01.09].
  29. http://ccdb.ucsd.edu/sao.html [accessed 15.01.09].
  30. http://ccdb.ucsd.edu/ [accessed 15.01.09].
  31. http://fireball.drexelmed.edu/birnlex/OWLDocs/ [accessed 15.01.09].
  32. http://www.nbirn.net/ [accessed 15.01.09].
  33. http://www.bioontology.org/wiki/index.php/CARO:Main_Page [accessed 15.01.09].
  34. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics. 2000;25(1):25–29
  35. http://obi.sourceforge.net/ [accessed 15.01.09].
  36. http://pdsp.med.unc.edu/ [accessed 15.01.09].
  37. http://www.w3.org/RDF/Validator/ [accessed 15.01.09].
  38. http://pellet.owldl.com/ [accessed 15.01.09].
  39. http://neuroweb.med.yale.edu/senselab/ [accessed 15.01.09].
  40. http://virtuoso.openlinksw.com/ [accessed 15.01.09].
  41. http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl [accessed 15.01.09].
  42. http://neuroweb.med.yale.edu/senselab/model-db.owl [accessed 15.01.09].
  43. http://neuroweb.med.yale.edu/senselab/brainpharm.owl [accessed 15.01.09].
  44. Marshall MS, Prud’hommeaux E. A prototype knowledge base for the life sciences, W3C interest group note. Web publication: http://www.w3.org/TR/hcls-kb/.
  45. http://neurocommons.org/ [accessed 15.01.09].
  46. Gangemi A, Guarino N, Masolo C, Oltramari A, Schneider L. Sweetening ontologies with DOLCE. In:  Gómez-Pérez A,  Benjamins VR editor. Proceedings of the 13th international conference on knowledge engineering and knowledge management. London, UK: Springer-Verlag; 2002;p. 166–181
  47. http://purl.org [accessed 15.01.09].
  48. http://www.oracle.com/database/ [accessed 15.01.09].
  49. http://www.w3.org/2001/sw/hcls/ [accessed 15.01.09].
  50. Cheung KH, Lim E, Samwald M, Chen H, Marenco L, Holford ME, et al. Approaches to neuroscience data integration. Briefings in Bioinformatics. 2009;10(4):345–353

PII: S0933-3657(09)00162-6

doi: 10.1016/j.artmed.2009.11.003

Artificial Intelligence in Medicine
Volume 48, Issue 1 , Pages 21-28 , January 2010