Context is Everything: Integrating Genomics, Epidemiological and Clinical Data Using GenEpiO Emma Griffiths Brinkman Lab Simon Fraser University, Burnaby, Canada On behalf of the GenEpiO Development Team Will Hsiao & Damion Dooley (BC Public Health Lab), Emma Griffiths & Fiona Brinkman (SFU) Sept 15, 2016 1
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Context is Everything: Integrating Genomics, Epidemiological and Clinical Data Using GenEpiO
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Context is Everything: Integrating Genomics, Epidemiological and Clinical
Data Using GenEpiO
Emma GriffithsBrinkman Lab
Simon Fraser University, Burnaby, Canada
On behalf of the GenEpiO Development TeamWill Hsiao & Damion Dooley (BC Public Health Lab),
Emma Griffiths & Fiona Brinkman (SFU)
Sept 15, 2016
Each year, one in eight Canadians (or 4 million people)
get sick with a domestically acquired food-borne illness.http://www.phac-aspc.gc.ca/efwd-emoha/efbi-emoa-eng.php
Slide courtesy of Will Hsiao
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Genomic sequences don’t mean much without contextual information.
• Must be combined with contextual information to make sense of the data… FAST!
Current Ontology Development Focuses On 3 Key Areas
Food Antimicrobial
Resistance
Disease Surveillance
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(FoodON)(SurvO) (ARO)
See draft version at https://github.com/GenEpiO/genepio/wiki
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Ontologies are commonly encoded using OWL (Web Ontology Language).
• Markup language for sharing ontologies on the web • Machine and human-readable• OWL statements written in RDF • Expressed in XML syntax
• Protégé (editor)• Ontology lookup services:
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Use ontology to identify common exposures, symptoms etc among genomics clusters
Example: Automating Case Definition generationCorrelate Genomics Salmonella Cluster A cases between 01 Mar 2014- 15 Mar 2014 with High-Risk Food Types Chicken Nuggets and Geographical Location of Vancouver
XXXXXXXXXXXXXXGenEpiO Will Help Integrate Genomics and
Epidemiological Data.
Genomic Epidemiology Ontology is like instrumentation for your contextual
information…it needs maintenance and continual
improvement
To achieve consensus and uptake International GenEpiO Consortium
European Bioinformatics InstituteMelanie CourtotHelen Parkinson
BC Public Laboratory and BC Centre for Disease Control (BCCDC)Damion DooleyJudy Isaac-RentonPatrick TangNatalie PrystajeckyJennifer GardyLinda HoangKim MacDonaldYin ChangEleni GalanisMarsha TaylorJennifer Law
University of MarylandLynn Schriml
Canadian Food Inspection Agency (CFIA)Adam KoziolBurton BlaisCatherine Carrillo