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 [email protected]http://www-staff.lboro.ac.uk/~lsrs1
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Abdulla, ICBO2011, Composite annotation for heart development
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Composite Annotation for Heart Development
Tariq Abdulla1, Ryan Imms1,
Jean-Marc Schleich2, Ron Summers1
ICBO 2011
1.Dept Electronic & Electrical Engineering, Loughborough University, UK2. LTSI, University of Rennes 1, [email protected]://www-staff.lboro.ac.uk/~lsrs1
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
OWLEquivalentTo: PATO:0001163 and (inheres_in some PR:000015308) and (contained_in some CL:0002350)
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In vitro EMT
Wildtype Notch1 BMP2
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.