This talk was given on June 28, 2009 at the Bio-Ontologies SIG as part of ISMB/ECCB 2009. You can download the paper this presentation is about from http://hdl.handle.net/10101/npre.2009.3286.1. More information on the ISMB conference is available at http://www.iscb.org/ismbeccb2009/ and http://friendfeed.com/ismbeccb2009

1. Annotation of SBML Models Through Rule-Based Semantic IntegrationBio-Ontologies SIG, ISMB 200928 June 2009Allyson Lister, Phillip Lord, Matthew Pocock, Anil WipatCISBAN and Newcastle Universityhttp://www.cisban.ac.uk/RBMhelpdesk@cisban.ac.uk Presentation slides covered under the CC-BY license

2. Telomeres and Ageing Image: Public Domain, NASA, from http://commons.wikimedia.org/wiki/File:Telomere_caps.gif

3. Checkpoint response to telomere uncapping in budding yeast Proctor et al. [1] Image and Model: [1]

5. Widely used (100+ tools)

6. Represents the mathematical model

9. Hard for a single modeller to retrieve all available knowledge

10. Most existing data integration tools are not suitable for modellers’ needs

12. A set of source ontologies, which are syntactic translations of data formats into OWL

13. Resolution of syntactic and semantic heterogeneity occurs separately

17. Provides syntactic transformation of data

18. But, not multiple XML files

20. Queries over the telomere ontology are written in SQWRL

21. SWRLTab and Jess are used to run these rules and queries

22. While writing rules/queries is mainly manual, running them is automatic

25. Results could be added back to the existing model

26. Cross-references

27. SBO annotations

28. Compartment localisations

29. Recommended name

31. Two were identified within the model, and were found by querying the telomere ontology

33. A two-step integration “rule-based mediation” helps model annotation

34. Off-the-shelf technology was used

35. Eases the task of fulfilling MIRIAM guidelines

36. SWRL rules were used to populate our semantically-rich telomere ontology

37. SQWRL was used for querying

39. Carole Proctor (10.1098/rsif.2006.0148)

40. Tom Kirkwood

41. Reviewers and conference organisersFunding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1‏

42. Thank you! xkcd.com Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1‏

43. References CJ Proctor, DA Lydall, RJ Boys, et al. Modelling the checkpoint response to telomere uncapping in budding yeast. Journal of The Royal Society Interface, Vol. 4, No. 12. (22 February 2007), pp. 73-90. AL Lister, M Pocock, A Wipat, Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models. Journal of Integrative Bioinformatics, Vol. 4, No. 3. (2007), 80. Stephan Philippi and Jacob Kohler. Addressing the problems with life-science databases for traditional uses and systems biology. Nature Reviews Genetics, 7(6):482–488, May 2006 W. Sujansky. Heterogeneous database integration in biomedicine. J Biomed Inform, 34(4):285–298, August 2001. Lincoln D Stein. Integrating biological databases. Nat Rev Genet, 4(5):337–345, May 2003. R. Alonso-Calvo et al. An agent- and ontology-based system for integrating public gene, protein, and disease databases. J Biomed Inform, 40(1):17–29, February 2007.

44. References Marie C. Rousset and Chantal Reynaud. Knowledge representation for information integration. Inf. Syst., 29(1):3–22, 2004. Li Xu and David W. Embley. Combining the Best of Global-as-View and Local-as-View for Data Integration. In Anatoly E. Doroshenko, Terry A. Halpin, Stephen W. Liddle, Heinrich C. Mayr, Anatoly E. Doroshenko, Terry A. Halpin, Stephen W. Liddle, and Heinrich C. Mayr, editors, ISTA, volume 48 of LNI, pages 123–136. GI, 2004. Natalya F. Noy and Mark A. Musen. The PROMPT suite: interactive tools for ontology merging and mapping. Int. J. Hum.-Comput. Stud., 59(6):983–1024, December 2003. HolgerWache et al. Ontology-based integration of information — a survey of existing approaches. In H. Stuckenschmidt, editor, Proceedings of the IJCAI’01 Workshop on Ontologies and Information Sharing, Seattle, Washington, USA, Aug 4-5, pages 108–117, 2001. JinguangGu, BaowenXu, and Xinmeng Chen. An XML query rewriting mechanism with multiple ontologies integration based on complex semantic mapping. Information Fusion, 9(4):512–522, October 2008.

45. Small Print This presentation is covered under the CC-BY 3.0 (http://creativecommons.org/licenses/by/3.0) license and can be found on slideshare at: The ontologies created by the authors are covered under the CC-BY 3.0 license, and external ontologies are governed under their own licensing requirements (specifically, SBO, which is covered under the Artistic License as defined on its SourceForge project site at http://sourceforge.net/projects/sbo/).

46. END