Applying Ontology Design Patterns in Bio-ontologies

  • Mikel Egaña
  • Alan Rector
  • Robert Stevens
  • Erick Antezana
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5268)


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.


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.


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  1. 1.
    Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Brief. Bioinformatics 7(3), 256–274 (2006)CrossRefGoogle Scholar
  2. 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. 3.
    Egaña, M., Antezana, E., Stevens, R.: Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. In: OWLed. (2008)Google Scholar
  4. 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)CrossRefGoogle Scholar
  5. 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)CrossRefGoogle Scholar
  6. 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. 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. 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)CrossRefGoogle Scholar
  9. 9.
    Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genetics 23, 25–29 (2000)Google Scholar
  10. 10.
    Horridge, M., Drummond, N., Goodwin, J., Rector, A., Stevens, R., Wang, H.: The Manchester OWL syntax. In: OWLed. (2006)Google Scholar
  11. 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. 12.
    Sirin, E., Parsia, B.: SPARQL-DL: SPARQL Query for OWL-DL. In: OWLED (2007)Google Scholar
  13. 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)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Mikel Egaña
    • 1
  • Alan Rector
    • 1
  • Robert Stevens
    • 1
  • Erick Antezana
    • 2
    • 3
  1. 1.School of Computer ScienceUniversity of ManchesterUK
  2. 2.Department of Plant Systems Biology, VIBGentBelgium
  3. 3.Department of Molecular GeneticsGent UniversityBelgium

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