Enriching the Gene Ontology via the Dissection of Labels Using the Ontology Pre-processor Language

  • Jesualdo Tomas Fernandez-Breis
  • Luigi Iannone
  • Ignazio Palmisano
  • Alan L. Rector
  • Robert Stevens
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6317)

Abstract

In this paper we describe the process of taking an axiomatically lean ontology and enriching it through the automatic application of axioms using ontology design patterns (ODP). Our exemplar is the Gene Ontology’s Molecular Function Ontology; this describes an important part of biology and is widely used to describe data. Yet much of the knowledge within the GO’s MF is captured within the term’s that label the concepts and within the natural language definitions for those concepts. Whilst both of these are absolutely necessary for an ontology, it is also useful to have the knowledge within the textual part of the ontology exposed for computational use. In this work we use an extension to the Ontology PreProcessor Language (OPPL) to dissect terms within the ontology and add axiomatisation, through OPPL’s application of ODP, that make the knowledge explicit for computational use. We show the axiomatic enriching of the GO MF; that this can be accomplished both rapidly and consistently; that there is an audit trail for the transformation; and that the queries supported by the ontology are greatly increased in number and complexity.

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References

  1. 1.
    Ogren, P., Cohen, K., Acquaah-Mensah, G., Eberlein, J., Hunter, L.: The Compositional Structure of Gene Ontology Terms. In: Pacific Symposium on Biocomputing, vol. 9, pp. 214–225 (2004)Google Scholar
  2. 2.
    GOConsortium: Gene ontology: tool for the unification of biology. Nature Genetics 25(1), 25–29 (2000)Google Scholar
  3. 3.
    Presutti, V., Gangemi, A.: Content ontology design patterns as practical building blocks for web ontologies. In: Li, Q., Spaccapietra, S., Yu, E., Olivé, A. (eds.) ER 2008. LNCS, vol. 5231, pp. 128–141. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  4. 4.
    Iannone, L., Rector, A.L., Stevens, R.: Embedding knowledge patterns into owl. In: Aroyo, L., Traverso, P., Ciravegna, F., Cimiano, P., Heath, T., Hyvönen, E., Mizoguchi, R., Oren, E., Sabou, M., Simperl, E. (eds.) ESWC 2009. LNCS, vol. 5554, pp. 218–232. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  5. 5.
    Egaña, M., Rector, A.L., Stevens, R., Antezana, E.: Applying ontology design patterns in bio-ontologies. In: Gangemi, A., Euzenat, J. (eds.) EKAW 2008. LNCS (LNAI), vol. 5268, pp. 7–16. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  6. 6.
    Solomon, W.D., Roberts, A., Rogers, J.E., Wroe, C.J., Rector, A.L.: Having our cake and eating it too: How the GALEN Intermediate Representation reconciles internal complexity with users’ requirements for appropriateness and simplicity. In: Overhage, J.M. (ed.) Proceedings of the 2000 American Medical Informatics Association Annual Symposium (AMIA 2000), Los Angeles, American Medical Informatics Association, pp. 819–823. Hanley and Belfus Inc. (2000)Google Scholar
  7. 7.
    Wroe, C., Stevens, R., Goble, C., Ashburner, M.: A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using DAML+OIL. In: 8th Pacific Symposium on biocomputing (PSB), pp. 624–636 (2003)Google Scholar
  8. 8.
    Rector, A.L.: Modularisation of domain ontologies implemented in description logics and related formalisms including owl. In: Proceedings of the 2nd International Conference on Knowledge Capture, Sanibel Island, USA (October 2003)Google Scholar
  9. 9.
    Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biology 6, R46 (2005)CrossRefGoogle Scholar
  10. 10.
    Horridge, M., Drummond, N., Godwin, J., Rector, A., Stevens, R., Wang, H.: The Manchester OWL Syntax. In: Proceedigns of OWLED 2006 OWL: Experiences and Directions, Athens GA, USA (2006)Google Scholar
  11. 11.
    de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., Steinbeck, C.: Chemical entities of biological interest: an update. Nucleic Acids Research 38(Suppl. 1:D249) (2010)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Jesualdo Tomas Fernandez-Breis
    • 1
  • Luigi Iannone
    • 2
  • Ignazio Palmisano
    • 2
  • Alan L. Rector
    • 2
  • Robert Stevens
    • 2
  1. 1.Departamento de Informatica y Sistemas Facultad de InformaticaUniversidad de MurciaMurciaSpain
  2. 2.School of Computer ScienceUniversity of ManchesterManchesterUnited Kingdom

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