1. Multiscale Information Modelling for Heart Morphogenesis Tariq Abdulla 13 th IMEKO TC1-TC7 Joint Symposium 02/09/2010

2. Outline  Heart Morphogenesis – what happens?  Information Modelling – what do we mean?  Multiscale Modelling - how do we do it?  Conclusion and Future Work

3. Heart Morphogenesis: what happens? Rear View

9. Outline  Heart Morphogenesis – what happens?  Information Modelling – what do we mean?  Multiscale Modelling - how do we do it?  Conclusion and Future Work

10. Information Modelling – what do we mean?  The concepts, relationships and constraints in a domain - these are ontologies  Use the same information models across multiple data sources  Thus we know how one piece of information relates to another

11. Basic Formal Ontology 11 Cell, Protein, Eye, Endocardial Cushion Red, Hypertrophic, Discontinuous Morphogenesis, Death, Development, Signaling, Growth

12. 12

13. Mammalian Phenotype Ontology

14. 14 Phenotype and Trait Ontology (PATO)

15. 15 Human Developmental Anatomy (EHDA)

16. 16 Post-composition

17. Outline  Heart Morphogenesis – what happens?  Information Modelling – what do we mean?  Multiscale Modelling - how do we do it?  Conclusion and Future Work

18. Multiscale Modelling – how do we do it?  Different types of computational model are suitable for different levels of biological scale  E.g. Biochemical reactions can be represented as networks or ODEs. Cellular behaviour can be modelled with agent based models.  Use models at one level of scale, to pass information to models at another level of scale

21. Conclusion and Future Work  Gene to phenotype annotation tends to use a surgical or anatomical perspective – but we know very little about mechanism or causes  Post-compositional annotation allows a link between multiscale measurement and multiscale modelling  Future plans include scale-linking between SBML models and agent based models, for simulation of Endocardial Cushion Growth

22. Questions?