building executable biological pathway models automatically from biopax
Post on 12-Sep-2014
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DESCRIPTION
LISC 2013 Presentation on translating BioPAX to Petri NetsTRANSCRIPT
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Timo Willemsen, Anton Feenstra, Paul Groth
[email protected] | @pgrothhttp://www.few.vu.nl/~pgroth
Building Executable Biological Pathway Models Automatically from BioPAX
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Outline
• Pathways• Modeling Pathways• Towards Executable Pathways• New Kinds of Semantics
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Biochemical Pathways, by Gerhard Michal – 1974 via http://blog.sciencemusings.com/2013/08/the-fire-that-burns-in-every-cell.html
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Online Pathway Databases
[Kelder et al. Nucleic Acids Research, 2012]
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http://wikipathways.org
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Modeling Pathways
• Interactions – Cells, genes, proteins
• Bio-chemical reactions
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Pathway:WP367
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BioPax
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Petri-nets for pathways
[Bonzann et al. 2009]
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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]
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PNML
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Building Executable Models
• Experiment in-silico• Static Dynamic Models• Formalism Gap
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BioPAX2PNMLArchitecture
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Conversion
https://github.com/TimoWillemsen/Biopax2PNML
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Results
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Future Work (data)
• Inference of edge weights using external datasets
• Determining additional interactions from non-pathway datasets
• More precise models using chemistry databases
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Future Work (System)
• Increase in validation rule sets• More complex pathways• A survey of wikipathways
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Summary
• Conversion of BioPAX to Petri Nets• Semantic checks for convertibility
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Semantics?
• +1 for interoperability• Are our semantics enough?• Moving towards models?• Connecting executable semantics to
declarative semantics