Skip to main content
View expanded cover

International Conference on Knowledge Engineering and Knowledge Management

EKAW 2008: Knowledge Engineering: Practice and Patterns pp 7–16Cite as

Applying Ontology Design Patterns in Bio-ontologies

  • Conference paper

Part of the Lecture Notes in Computer Science book series (LNAI,volume 5268)

Abstract

Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent “modifiers” of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it.

Keywords

  • Gene Ontology
  • Object Property
  • Biological Knowledge
  • SPARQL Query
  • Independent Entity

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-3-540-87696-0_4
  • Chapter length: 10 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   89.00
Price excludes VAT (USA)
  • ISBN: 978-3-540-87696-0
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Brief. Bioinformatics 7(3), 256–274 (2006)

    CrossRef  Google Scholar 

  2. Pressuti, V., Gangemi, A., David, S., de Cea, G.A., Suárez-Figueroa, M., Montiel-Ponsoda, E., Poveda, M.: A Library of Ontology Design Patterns. NeOn Deliverable 2.5.1 (2008)

    Google Scholar 

  3. Egaña, M., Antezana, E., Stevens, R.: Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. In: OWLed. (2008)

    Google Scholar 

  4. Gangemi, A.: Ontology Design Patterns for Semantic Web Content. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 262–276. Springer, Heidelberg (2005)

    CrossRef  Google Scholar 

  5. Aranguren, M.E., Antezana, E., Kuiper, M., Stevens, R.: Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC bioinformatics 9 (suppl. 5), S1 (2008)

    CrossRef  Google Scholar 

  6. Brockmans, S., Volz, R., Eberhart, A., Löffler, P.: Visual Modelling of OWL DL Ontologies using UML. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 198–213. Springer, Heidelberg (2004)

    Google Scholar 

  7. Grenon, P., Smith, B., Goldberg, L.: Biodynamic Ontology: Applying BFO in the Biomedical Domain. In: Pisanelli, D.M. (ed.) Ontologies in Medicine, pp. 20–38. IOS Press, Amsterdam (2004)

    Google Scholar 

  8. Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., Schneider, L.: Sweetening ontologies with DOLCE. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS(LNAI), vol. 2473, pp. 166–182. Springer, Heidelberg (2002)

    CrossRef  Google Scholar 

  9. Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genetics 23, 25–29 (2000)

    Google Scholar 

  10. Horridge, M., Drummond, N., Goodwin, J., Rector, A., Stevens, R., Wang, H.: The Manchester OWL syntax. In: OWLed. (2006)

    Google Scholar 

  11. Vrandecić, D.: Explicit Knowledge Engineering Patterns with Macros. In: Welty, C., Gangemi, A. (eds.) Ontology Patterns for the Semantic Web Workshop (ISWC) (2005)

    Google Scholar 

  12. Sirin, E., Parsia, B.: SPARQL-DL: SPARQL Query for OWL-DL. In: OWLED (2007)

    Google Scholar 

  13. Aranguren, M.E., Wroe, C., Goble, C., Stevens, R.: In situ migration of handcrafted ontologies to reason-able forms. Data and Knowledge Engineering 66(1), 147–162 (2008)

    CrossRef  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Computer Science, University of Manchester, UK

    Mikel Egaña, Alan Rector & Robert Stevens

  2. Department of Plant Systems Biology, VIB, Gent, Belgium

    Erick Antezana

  3. Department of Molecular Genetics, Gent University, Belgium

    Erick Antezana

Authors
  1. Mikel Egaña
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alan Rector
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert Stevens
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Erick Antezana
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

    Rights and permissions

    Reprints and Permissions

    Copyright information

    © 2008 Springer-Verlag Berlin Heidelberg

    About this paper

    Cite this paper

    Egaña, M., Rector, A., Stevens, R., Antezana, E. (2008). Applying Ontology Design Patterns in Bio-ontologies. In: Gangemi, A., Euzenat, J. (eds) Knowledge Engineering: Practice and Patterns. EKAW 2008. Lecture Notes in Computer Science(), vol 5268. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87696-0_4

    Download citation

    • DOI: https://doi.org/10.1007/978-3-540-87696-0_4

    • Publisher Name: Springer, Berlin, Heidelberg

    • Print ISBN: 978-3-540-87695-3

    • Online ISBN: 978-3-540-87696-0

    • eBook Packages: Computer ScienceComputer Science (R0)