What We Have Gluing Structure - Qualitative Aspects Gluing Numbers - Quantitative Aspects

Systems Biology Pathway Exchange (SBPAX) Gluing SBML-type Models to BioPAX-type Pathways

Oliver Ruebenacker

Virtual Cell, Center for Cell Analysis and Modelling BioPAX-OBO

Workshop on Ontologies of Cellular Networks, March 27-28, 2007

Ruebenacker SBPAX What We Have Gluing Structure - Qualitative Aspects Gluing Numbers - Quantitative Aspects Outline

1 What We Have What is At Stake What Has Been Done

2 Gluing Structure - Qualitative Aspects Building a SBML/BioPAX Joint Repository The System Model Species and Physical Entities Reactions and Conversions

3 Gluing Numbers - Quantitative Aspects Reactions and Reaction Models Real and Effective Stoichiometry

Ruebenacker SBPAX What We Have What is At Stake Gluing Structure - Qualitative Aspects What Has Been Done Gluing Numbers - Quantitative Aspects SBML and BioPAX

SBML BioPAX “System Biological Markup “Biological Pathway Language” Exchange” Kinetic Modelling Qualitative, no kinetics XML RDF reactions, species interactions, physical entities No term hierarchy Hierarchy of Terms

The SBML-BioPAX Integration Challenge Motivation: Both communities possess enormous amounts of public data on cellular reaction networks. Challenge: Purposes have been diverging and therefore terms are incompatible.

Ruebenacker SBPAX What We Have What is At Stake Gluing Structure - Qualitative Aspects What Has Been Done Gluing Numbers - Quantitative Aspects Conversions and Annotations

Conversions Annotation e.g. Binom (Cytoscape), e.g. J Luciano and J Zucker sbml2biopax (sbml.org) Use BioPAX for annotations file ⇔ file in SBML reaction ⇔ conversion Add info about conversion or physical entity to species species ⇔ physicalEntity or reaction

How Far We Get With Conversions And Annotations Pro: One-to-one map between SBML and BioPAX often considered useful Contra: In general, one-to-one map is wrong

Ruebenacker SBPAX Building a SBML/BioPAX Joint Repository What We Have The System Model Gluing Structure - Qualitative Aspects Species and Physical Entities Gluing Numbers - Quantitative Aspects Reactions and Conversions SBML-SBPAX-BioPAX Repository

Requirements Relationships between SBML and BioPAX terms. Terms compatible with both SBML and BioPAX Identify and reconcile semantic differences

SBML-SBPAX-BioPAX Joint RDF Repository

SBML SBPAX BioPAX SBML data Relationships BioPAX data objects (RDF between SBML and objects Reflection) BioPAX objects

Ruebenacker SBPAX Building a SBML/BioPAX Joint Repository What We Have The System Model Gluing Structure - Qualitative Aspects Species and Physical Entities Gluing Numbers - Quantitative Aspects Reactions and Conversions System Model

BioPAX SBML There is no model File boundaries delineate models File boundaries not delineations

System Model (SBPAX) Introduce term system model System model links to its components Advantage: Easy to re-use objects for different models

Ruebenacker SBPAX Building a SBML/BioPAX Joint Repository What We Have The System Model Gluing Structure - Qualitative Aspects Species and Physical Entities Gluing Numbers - Quantitative Aspects Reactions and Conversions Species and Physical Entities

Physical Entity (BioPAX)

Species (SBML) Hybrid ID specs No ID restrictions ID by sequence for DNA, RNA, proteins Compartment hierarchy ID by chemical structure for Species can be anything “small molecule” Species depend on model ID unclear for complexes No compartment hierarchy

Substance (SBPAX) Hierarchy of substance IDs: Sequence, chemical structure, organism, location

Ruebenacker SBPAX Building a SBML/BioPAX Joint Repository What We Have The System Model Gluing Structure - Qualitative Aspects Species and Physical Entities Gluing Numbers - Quantitative Aspects Reactions and Conversions Reactions and Conversions

Reaction (SBML) Conversion (BioPAX) Continuous flux from pool Discrete event, discrete to pool participants Controls included Controls separate objects

Reactions (SBPAX) Distinguish between individual reaction and reaction ensemble Substance hierarchy ⇒ Reaction hierarchy Terms for controls

Ruebenacker SBPAX What We Have Reactions and Reaction Models Gluing Structure - Qualitative Aspects Real and Effective Stoichiometry Gluing Numbers - Quantitative Aspects Reactions and Reaction Models

Reaction (SBML) Conversion (BioPAX) Kinetic No kinetics Approximate rate laws No approximations Modeller’s choices No choices

Reaction and Reaction Model (SBPAX) Need to distinguish between reaction and reaction model Reaction only objective truths, no approximations or modeller’s choices Reaction Model includes kinetics, which are approximate and contain modeller’s choices

Ruebenacker SBPAX What We Have Reactions and Reaction Models Gluing Structure - Qualitative Aspects Real and Effective Stoichiometry Gluing Numbers - Quantitative Aspects Stoichiometry

SBML BioPAX Stoichiometry merely rate Actual numbers of law book keeping participants

SBPAX Distinguish between real and effective stoichiometry Objective real numbers of participants Effective stoichiometry can be any multiple

Ruebenacker SBPAX What We Have Reactions and Reaction Models Gluing Structure - Qualitative Aspects Real and Effective Stoichiometry Gluing Numbers - Quantitative Aspects Acknowledgements

BioPAX-OBO Alan Ruttenberg BioPAX @ Virtual Cell Elgar Pichler Michael Blinov Joanne Luciano Ion Moraru Jonathan Rees Jim Schaff Andrea Splendiani Michel Dumontier Jeremy Zucker

Ruebenacker SBPAX