building executable biological pathway models automatically from biopax

Timo Willemsen, Anton Feenstra, Paul Groth

p.t.groth@vu.nl | @pgrothhttp://www.few.vu.nl/~pgroth

Building Executable Biological Pathway Models Automatically from BioPAX

Outline

• Pathways• Modeling Pathways• Towards Executable Pathways• New Kinds of Semantics

Biochemical Pathways, by Gerhard Michal – 1974 via http://blog.sciencemusings.com/2013/08/the-fire-that-burns-in-every-cell.html

Online Pathway Databases

[Kelder et al. Nucleic Acids Research, 2012]

http://wikipathways.org

Modeling Pathways

• Interactions – Cells, genes, proteins

• Bio-chemical reactions

Pathway:WP367

BioPax

Petri-nets for pathways

[Bonzann et al. 2009]

Usefulness

“… C.elegans vulval development, reproducing several in vivo experiments. We generated insightful and testable predictions involving the microRNA mir-61”

[Bonzann et al. 2009]

PNML

Building Executable Models

• Experiment in-silico• Static Dynamic Models• Formalism Gap

BioPAX2PNMLArchitecture

Conversion

https://github.com/TimoWillemsen/Biopax2PNML

Results

Future Work (data)

• Inference of edge weights using external datasets

• Determining additional interactions from non-pathway datasets

• More precise models using chemistry databases

Future Work (System)

• Increase in validation rule sets• More complex pathways• A survey of wikipathways

Summary

• Conversion of BioPAX to Petri Nets• Semantic checks for convertibility

Semantics?

• +1 for interoperability• Are our semantics enough?• Moving towards models?• Connecting executable semantics to

declarative semantics