Presentation on theme: "Composite Annotation for Heart Development Tariq Abdulla 1, Ryan Imms 1, Jean-Marc Schleich 2, Ron Summers 1 ICBO 2011 1.Dept Electronic & Electrical Engineering,"— Presentation transcript:
Composite Annotation for Heart Development Tariq Abdulla 1, Ryan Imms 1, Jean-Marc Schleich 2, Ron Summers 1 ICBO 2011 1.Dept Electronic & Electrical Engineering, Loughborough University, UK 2. LTSI, University of Rennes 1, France R.Summers@lboro.ac.uk http://www-staff.lboro.ac.uk/~lsrs1
Outline Heart Development – what happens? Anatomy, Tissue, Cell, Protein Multiscale Modelling Pre-composition: GO, MP Post-composition: PATO, OPB Conclusions
12 Compucell3D and an SBML Solver BionetSolver CC3D Concentration of a subcellular species (SBML) determines cell type (CC3D) CC3D BionetSolver Cell type (CC3D) determines value for rate parameters in the subcellular model (SBML)
Conclusions Gene to phenotype annotation tends to use a surgical or anatomical perspective – but does not directly include mechanism or causes By including cell and protein level annotations, causes and mechanisms are more explicit Post-composition enables more flexible annotation. But it is more difficult for annotators. The two strategies can be combined, but some post- composition seems necessary for multiscale and development research In development, we can’t ignore the structure of cells For multiple scales, there are too many combinations to pre-compose them all Lightweight reference ontologies are more manageable, but repositories of post-composed annotations are more challenging for reasoning
Ackowledgements Randy Heiland Maciej Swat Lucile Houyel Jean-Marc Schleich Ron Summers Fanny Bajolle Dan Cook John Gennari Ryan Roper
In vitro EMT WildtypeNotch1BMP2 L. Luna-zurita et al. “Integration of a Notch-dependent mesenchymal gene program and Bmp2-driven cell invasiveness regulates murine cardiac valve formation,” The Journal of Clinical Investigation, vol. 120, 2010.