Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Building Executable Biological Pathway Models Automatically from BioPAX

1,201 views

Published on

LISC 2013 Presentation on translating BioPAX to Petri Nets

Published in: Technology, Business

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

×