Building Executable Biological Pathway Models Automatically from BioPAX

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LISC 2013 Presentation on translating BioPAX to Petri Nets

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  • “Biological pathways are often used to abstract and modularize our knowledge about molecu- lar biology. A pathway organizes our knowledge with respect to a functional mechanism and describes events at the molecular level that compose this mechanism “ - (exploratory Pathway Analysis ) Thomas Kelder
  • Kegg, genmapp, pathway commons
  • Talk about what wikipathways offers?
  • C. elegans Programmed Cell Death Pathway
  • “Supports metabolic pathways, signaling pathways (including states of molecules and generic molecules), gene regulatory networks, molecular interactions, genetic interactions.”OwlPrimarily about semantic types and drawing”
  • 600 nodes – 1000 arcsSeveral months for constructionIntrdocue petri-nets here
  • Issues with drawing
  • Say something about sparqlIssue is that many wikipathways are still not there
  • This is easy
  • yasper
  • Excecutability – what do we need to do there?
  • Building Executable Biological Pathway Models Automatically from BioPAX

    1. 1. Building Executable Biological Pathway Models Automatically from BioPAX Timo Willemsen, Anton Feenstra, Paul Groth p.t.groth@vu.nl | @pgroth http://www.few.vu.nl/~pgroth
    2. 2. Outline • • • • Pathways Modeling Pathways Towards Executable Pathways New Kinds of Semantics
    3. 3. Biochemical Pathways, by Gerhard Michal – 1974 via http://blog.sciencemusings.com/2013/08/the-fire-that-burns-in-every-cell.html
    4. 4. Online Pathway Databases [Kelder et al. Nucleic Acids Research, 2012]
    5. 5. http://wikipathways.org
    6. 6. Modeling Pathways • Interactions – Cells, genes, proteins • Bio-chemical reactions
    7. 7. Pathway:WP367
    8. 8. BioPax
    9. 9. Petri-nets for pathways [Bonzann et al. 2009]
    10. 10. Usefulness “… C.elegans vulval development, reproducing several in vivo experiments. We generated insightful and testable predictions involving the microRNA mir61” [Bonzann et al. 2009]
    11. 11. PNML
    12. 12. Building Executable Models • Experiment in-silico • Static  Dynamic Models • Formalism Gap
    13. 13. BioPAX2PNML Architecture
    14. 14. Conversion https://github.com/TimoWillemsen/Biopax2PNML
    15. 15. Results
    16. 16. Future Work (data) • Inference of edge weights using external datasets • Determining additional interactions from non-pathway datasets • More precise models using chemistry databases
    17. 17. Future Work (System) • Increase in validation rule sets • More complex pathways • A survey of wikipathways
    18. 18. Summary • Conversion of BioPAX to Petri Nets • Semantic checks for convertibility
    19. 19. Semantics? • • • • +1 for interoperability Are our semantics enough? Moving towards models? Connecting executable semantics to declarative semantics

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