Annotation of SBML Models Through Rule-Based Semantic IntegrationBio-Ontologies SIG, ISMB 200928 June 2009Allyson Lister, ...
Telomeres and Ageing<br />Image: Public Domain, NASA, from http://commons.wikimedia.org/wiki/File:Telomere_caps.gif<br />
Checkpoint response to telomere uncapping in budding yeast<br />Proctor et al. [1]<br />Image and Model: [1]<br />
What is SBML?<br /><ul><li>Standard format
Widely used (100+ tools)
Represents the mathematical model
Enables linking to the underlying biology</li></li></ul><li>Model Annotation Life Cycle<br />Get data<br />Read literature...
Challenges in Model Annotation<br /><ul><li>Knowledge in lots of places
Hard for a single modeller to retrieve all available knowledge
Most existing data integration tools are not suitable for modellers’ needs
Many integration methods are purely syntactic</li></li></ul><li>Rule-Based Mediation<br /><ul><li>A core ontology, which i...
A set of source ontologies, which are syntactic translations of data formats into OWL
Resolution of syntactic and semantic heterogeneity occurs separately
Can use existing, independent ontologies</li></li></ul><li>Where is the knowledge?<br /><ul><li>Input data sources: UniPro...
Data can end up in SBML format via MFO [2]</li></li></ul><li>How are the data sources integrated?<br />XML<br />OWL<br />U...
Achieving the XML to OWL Conversion<br /><ul><li>The XMLTab plugin for Protégé quickly creates classes and instances from XML
Provides syntactic transformation of data
But, not multiple XML files
May not be in active development</li></li></ul><li>Syntactic Ontologies ->Telomere Ontology<br /><ul><li>Rules written in ...
Queries over the telomere ontology are written in SQWRL
SWRLTab and Jess are used to run these rules and queries
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Annotation of SBML Models Through Rule-Based Semantic Integration

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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

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  • At CISBAN, part of our research focuses on telomeres and their relationship to ageing. The model chosen for the use cases involves telomere shortening.From [1]: “Telomeres are repetitive sequences of DNA situated at the ends of linear chromosomes. They require protection from being recognized as double-strand breaks to prevent activation of the DNA damage response.” They shorten with each cell division, and are implicated in ageing.
  • This model of telomere uncapping is written in SBML. But what is SBML? At a minimum, SBML models will contain all the maths needed to run the simulations. Linking to biology is not required and therefore many biologist tend to leave this part out. Any integration procedure needs to add information of this type.
  • It’s difficult to create models, even with available tools.
  • Annotation of SBML Models Through Rule-Based Semantic Integration

    1. 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<br />Presentation slides covered under the CC-BY-SA 2.5<br />
    2. 2. Telomeres and Ageing<br />Image: Public Domain, NASA, from http://commons.wikimedia.org/wiki/File:Telomere_caps.gif<br />
    3. 3. Checkpoint response to telomere uncapping in budding yeast<br />Proctor et al. [1]<br />Image and Model: [1]<br />
    4. 4. What is SBML?<br /><ul><li>Standard format
    5. 5. Widely used (100+ tools)
    6. 6. Represents the mathematical model
    7. 7. Enables linking to the underlying biology</li></li></ul><li>Model Annotation Life Cycle<br />Get data<br />Read literature<br />(Re)build model<br />Parameterise <br />Examine results<br />Run and test model<br />
    8. 8. Challenges in Model Annotation<br /><ul><li>Knowledge in lots of places
    9. 9. Hard for a single modeller to retrieve all available knowledge
    10. 10. Most existing data integration tools are not suitable for modellers’ needs
    11. 11. Many integration methods are purely syntactic</li></li></ul><li>Rule-Based Mediation<br /><ul><li>A core ontology, which is a semantically-rich description of the research domain of interest
    12. 12. A set of source ontologies, which are syntactic translations of data formats into OWL
    13. 13. Resolution of syntactic and semantic heterogeneity occurs separately
    14. 14. Can use existing, independent ontologies</li></li></ul><li>Where is the knowledge?<br /><ul><li>Input data sources: UniProtKB, BioGRID, Pathway Commons
    15. 15. Data can end up in SBML format via MFO [2]</li></li></ul><li>How are the data sources integrated?<br />XML<br />OWL<br />UniprotKB<br />XML<br />OWL<br />Instances<br />MFO<br />BioGRID<br />Telomere<br />Ontology<br />OWL<br />PathwayCommons<br />Resolve<br />syntactic<br />heterogeneity<br />Resolve<br />semantic<br />heterogeneity<br />Retrieve<br />data<br />Export<br />to<br />SBML<br />Reviews of integration types [3-6] <br />Reviews for ontology mapping [7-11]<br />
    16. 16. Achieving the XML to OWL Conversion<br /><ul><li>The XMLTab plugin for Protégé quickly creates classes and instances from XML
    17. 17. Provides syntactic transformation of data
    18. 18. But, not multiple XML files
    19. 19. May not be in active development</li></li></ul><li>Syntactic Ontologies ->Telomere Ontology<br /><ul><li>Rules written in SWRL
    20. 20. Queries over the telomere ontology are written in SQWRL
    21. 21. SWRLTab and Jess are used to run these rules and queries
    22. 22. While writing rules/queries is mainly manual, running them is automatic
    23. 23. Semantic value is added to the information by mapping it to a semantically-rich core ontology</li></li></ul><li>Mappings from UniProtKB<br />upkb:locationSlot(?s, ?l) ˄<br />upkb:Text(?l, ?value) ˄<br />swrlb:equal(?value, “Nucleus”) -><br />tuo:Nucleus(?l)<br />
    24. 24. What is RAD9?<br /><ul><li>Tell me about something called ‘rad9’
    25. 25. Results could be added back to the existing model
    26. 26. Cross-references
    27. 27. SBO annotations
    28. 28. Compartment localisations
    29. 29. Recommended name
    30. 30. These results allow the addition of information required by the MIRIAM guidelines</li></li></ul><li>What interacts with RAD9?<br /><ul><li>In Proctor et al., there are four interacting partners with RAD9
    31. 31. Two were identified within the model, and were found by querying the telomere ontology
    32. 32. Of the unknown partners, one was provisionally identified as MEC1.</li></li></ul><li>Summary<br /><ul><li>SBML models require large amounts of data to be mathematically and biologically complete
    33. 33. A two-step integration “rule-based mediation” helps model annotation
    34. 34. Off-the-shelf technology was used
    35. 35. Eases the task of fulfilling MIRIAM guidelines
    36. 36. SWRL rules were used to populate our semantically-rich telomere ontology
    37. 37. SQWRL was used for querying
    38. 38. We found new knowledge that the modeller was not aware of</li></li></ul><li>http://www.cisban.ac.uk/RBM<br /><ul><li>Phillip Lord, Matthew Pocock, Anil Wipat
    39. 39. Carole Proctor (10.1098/rsif.2006.0148)
    40. 40. Tom Kirkwood
    41. 41. Reviewers and conference organisers</li></ul>Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1‏<br />
    42. 42. Thank you!<br />xkcd.com<br />Funding for CISBAN provided by BBSRC/EPSRC grant ref BB/C008200/1‏<br />
    43. 43. References<br />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. <br />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.<br />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<br />W. Sujansky. Heterogeneous database integration in biomedicine. J Biomed Inform, 34(4):285–298, August 2001.<br />Lincoln D Stein. Integrating biological databases. Nat Rev Genet, 4(5):337–345, May 2003.<br />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.<br />
    44. 44. References<br />Marie C. Rousset and Chantal Reynaud. Knowledge representation for information integration. Inf. Syst., 29(1):3–22, 2004.<br />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.<br />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.<br />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.<br />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. <br />
    45. 45. Small Print<br />This presentation is covered under the CC-BY-SA 2.5 (http://creativecommons.org/licenses/by-sa/2.5/ ) license and can be found on slideshareat: http://www.slideshare.net/allysonlister/annotation-of-sbml-models-through-rulebased-semantic-integration<br />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/).<br />
    46. 46. END<br />

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