OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences

  • Christine Golbreich
  • Matthew Horridge
  • Ian Horrocks
  • Boris Motik
  • Rob Shearer
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4825)

Abstract

OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively informal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semantic Web reasoners can be used to efficiently reason with OBO ontologies. Furthermore, we show that grounding the OBO language in formal semantics is useful for the ontology development process: using an OWL reasoner, we detected a likely modeling error in one OBO ontology.

References

  1. 1.
    Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene Ontolgy: Tool for the Unification of Biology. Nature Genetics 25(1), 25–29 (2000)CrossRefGoogle Scholar
  2. 2.
    Derriere, S., Richard, A., Preite-Martinez, A.: An Ontology of Astronomical Object Types for the Virtual Observatory. In: Proc. of the 26th meeting of the IAU: Virtual Observatory in Action: New Science, New Technology, and Next Generation Facilities, Prague, Czech Republic, August 21–22, 2006, pp. 17–18 (2006)Google Scholar
  3. 3.
    Donini, F.M., Nardi, D., Rosati, R.: Description Logics of Minimal Knowledge and Negation as Failure. ACM Transactions on Computational Logic 3(2), 177–225 (2002)CrossRefMathSciNetGoogle Scholar
  4. 4.
    Gardiner, T., Horrocks, I., Tsarkov, D.: Automated Benchmarking of Description Logic Reasoners. In: Proc. of DL 2006. CEUR, vol. 189 (2006)Google Scholar
  5. 5.
    Golbreich, C., Zhang, S., Bodenreider, O.: The Foundational Model of Anatomy in OWL: Experience and Perspectives. Journal of Web Semantics 4(3), 181–195 (2006)Google Scholar
  6. 6.
    Goodwin, J.: Experiences of using OWL at the Ordnance Survey. In: Proc. of OWL-ED 2005. CEUR, vol. 188 (2005)Google Scholar
  7. 7.
    Grau, B.C., Horrocks, I., Kazakov, Y., Sattler, U.: Just the Right Amount: Extracting Modules from Ontologies. In: Proc. of WWW 2007, pp. 717–726 (2007)Google Scholar
  8. 8.
    Haarslev, V., Möller, R.: RACER System Description. In: Goré, R.P., Leitsch, A., Nipkow, T. (eds.) IJCAR 2001. LNCS (LNAI), vol. 2083, pp. 701–706. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  9. 9.
    Hartel, F.W., de Coronado, S., Dionne, R., Fragoso, G., Golbeck, J.: Modeling a Description Logic Vocabulary for Cancer Research. Journal of Biomedical Informatics 38(2), 114–129 (2005)CrossRefGoogle Scholar
  10. 10.
    Horridge, M., Bechhofer, S., Noppens, O.: Igniting the OWL 1.1 Touch Paper: The OWL API. In: Proc. OWL-ED 2007. CEUR, vol. 258 (2007)Google Scholar
  11. 11.
    Kalyanpur, A., Parsia, B., Hendler, J.: A Tool for Working with Web Ontologies. International Journal on Semantic Web and Information Systems 1(1), 36–49 (2005)Google Scholar
  12. 12.
    Kalyanpur, A., Parsia, B., Sirin, E., Hendler, J.: Debugging Unsatisfiable Classes in OWL Ontologies. Journal of Web Semantics 3(4), 243–366 (2005)Google Scholar
  13. 13.
    Knublauch, H., Fergerson, R.W., Noy, N.F., Musen, M.A.: The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 229–243. Springer, Heidelberg (2004)Google Scholar
  14. 14.
    Lacy, L., Aviles, G., Fraser, K., Gerber, W., Mulvehill, A., Gaskill, R.: Experiences Using OWL in Military Applications. In: Proc. of OWL-ED 05. CEUR, vol. 188 (2005)Google Scholar
  15. 15.
    Motik, B., Horrocks, I., Sattler, U.: Bridging the Gap Between OWL and Relational Databases. In: Proc. of WWW 2007, pp. 807–816 (2007)Google Scholar
  16. 16.
    Motik, B., Sattler, U.: A Comparison of Reasoning Techniques for Querying Large Description Logic ABoxes. In: Hermann, M., Voronkov, A. (eds.) LPAR 2006. LNCS (LNAI), vol. 4246, pp. 227–241. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  17. 17.
    Motik, B., Shearer, R., Horrocks, I.: Optimized Reasoning in Description Logics using Hypertableaux. In: Proc. of CADE-21. LNCS (LNAI), vol. 4603, pp. 67–83. Springer, Heidelberg (2007)Google Scholar
  18. 18.
    Patel-Schneider, P.F., Horrocks, I.: OWL 1.1 Web Ontology Language Overview. W3C Member Submission (December 19, 2006), Available at http://www.w3.org/Submission/owl11-overview/
  19. 19.
    Quillian, M.R.: Semantic Memory. In: Minsky, M. (ed.) Semantic Information Processing, pp. 216–270. MIT Press, Cambridge, MA, USA (1968)Google Scholar
  20. 20.
    Rector, A., Rogers, J.: Ontological and Practical Issues in Using a Description Logic to Represent Medical Concept Systems: Experience from GALEN. In: Reasoning Web, Second International Summer School, Tutorial Lectures, Lisbon, Portugal, September 4–8 2006, pp. 197–231 (2006)Google Scholar
  21. 21.
    Ruttenberg, A., Rees, J., Luciano, J.: Experience Using OWL DL for the Exchange of Biological Pathway Information. In: Proc. of OWL-ED 2005. CEUR, vol. 188 (2005)Google Scholar
  22. 22.
    Sidhu, A., Dillon, T., Chang, E., Sidhu, B.S.: Protein Ontology Development using OWL. In: Proc. of OWL-ED 2005. CEUR, vol. 188 (2005)Google Scholar
  23. 23.
    Sirin, E., Parsia, B.: Pellet: An OWL DL Reasoner. In: Proc. of DL 2004. CEUR, vol. 104 (2004)Google Scholar
  24. 24.
    Soergel, D., Lauser, B., Liang, A., Fisseha, F., Keizer, J., Katz, S.: Reengineering Thesauri for New Applications: The AGROVOC Example. Journal of Digital Information 4(4) (2004)Google Scholar
  25. 25.
    Tsarkov, D., Horrocks, I.: FaCT++ Description Logic Reasoner: System Description. In: Furbach, U., Shankar, N. (eds.) IJCAR 2006. LNCS (LNAI), vol. 4130, pp. 292–297. Springer, Heidelberg (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Christine Golbreich
    • 1
  • Matthew Horridge
    • 2
  • Ian Horrocks
    • 3
  • Boris Motik
    • 3
  • Rob Shearer
    • 3
  1. 1.University of Versailles Saint-Quentin, 55 avenue de Paris, 78035 VersaillesFrance
  2. 2.School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PLUK
  3. 3.Oxford University Computing Laboratory, Wolfson Building, Parks Road, Oxford, OX1 3QDUK

Personalised recommendations