AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November.

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Presentation transcript:

AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November 28, 2008

2 Components controlling structure & function of DNA

3 Decondensed chromatin Condensed chromatin Histone methylation at H3K9 DNA methylation HDAC HAT Histone acetylation Extending my biological model

4 My brain is too small!

5 Empower me with a virtual brain My ws Your ws My ws Your ws My ws * From P.J. Verschure, Journal of Cellular Biochemistry 2006, vol. 99(1), pg *

6 Workflow and Semantic Web Quer y Retrieve documents from Medline Extract gene or protein names Calculate ranking scores Create biological cross references Convert to table (html) Add documents (IDs) to semantic model Add proteins to semantic model Add scores to semantic model Add cross references to semantic model Add query to semantic model Extract gene or protein interactions Add gene or protein interactions to semantic model

7 Separation of models and instances in OWL

AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November 28, 2008