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AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November 28, 2008 Components controlling structure & function of DNA 2 Extending my biological model Decondensed chromatin HDAC HAT Histone acetylation Histone methylation at H3K9 DNA methylation Condensed chromatin 3 My brain is too small! 4 Empower me with a ‘virtual brain’ * My ws Your ws My ws My ws Your ws 5 * From P.J. Verschure, Journal of Cellular Biochemistry 2006, vol. 99(1), pg 23-34 Workflow and Semantic Web Quer y Decondensed chromatin HDAC Add query to semantic model Retrieve documents from Medline HAT Histone acetylation Histone methylation at H3K9 DNA methylation Condensed chromatin Add documents (IDs) to semantic model Extract gene or protein names Add proteins to semantic model Extract gene or protein interactions Add gene or protein interactions to semantic model Calculate ranking scores Add scores to semantic model Create biological cross references Add cross references to semantic model Convert to table (html) 6 Separation of models and instances in OWL BiologicalModel Proteins or genes association assertion isComponentOf some Document isComponentOf some relates some relatesBy some Association Protein term Protein or gene PMID: 15298701 “HDAC1” Interaction term “p68 and p72 associate with histone deacetylase 1 (HDAC1)” “p68” “associate” isComponentOf HDAC1-PCAF interaction PCAF HDAC1 isComponentOf Retrieved document Document search query Protein or gene Discovered protein term Discovered interaction term Text mining process Document search query PMID: 15298701 Discovered protein term Chromatin condensation hypothesis HDAC1-p68 association “HDAC1” HDAC1 “p68” “interacts” “DNMT3B also interacts with histone deacetylase 1 (HDAC1)” discoveredBy searchesWith discoveredBy discoveredBy discoveredBy Discovered association assertion Interaction Discovered interaction assertion AIDA based extraction process relates relates BiologicalModel “HDAC1 AND chromatin” relatesBy isComponentOf Chromatin condensation hypothesis p68 “p68” “p68 and p72 associate with histone deacetylase 1 (HDAC1)” 7 AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November 28, 2008
