Populating the Common Biorepository Model with caTissue Suite 2.0 Data - Demo Dave Mulvihill January 2012

Background The goal for a Common Biorepository Model (CBM) is to reduce the time and effort required by researchers to locate a biobank that has the specimens they need ETL scripts have been provided with caTissue Suite v2.0 to populate the CBM database Summary level data

Procedure pository+Model+Database pository+Model+Database Many transformations called by 4 ETL Jobs 1.CPAvailability a)Requires user/data owner intervention 2.Organization 3.CollectionProtocol Data 4.Collection Summary Data

CP Availability Process Run CPAvailability ETL Job Set CP mask flag, specimen and annotation values in Excel file Run CPAvailability ETL Job Final transformation used in downstream ETL jobs Note: Subsequent runs of the ETL job compares previous profile responses to current Collection Protocols Start caTissue Updated

Testing Scenarios Verify data in preCPAvailabilityMapping.xls Verify data in CPAvailAnnotationMapping.xls – Annotation Availability Profile ID – Specimen Availability Summary Profile ID Verify all tables populated by ETL – Tables listed in documentation

Known Issues CBM team resolving “Not Specified” diagnosis, specimen type and anatomic location. SQL Join for caTissue Oracle database will need to be set manually (this will be added to the documentation) Issue with caTissue -> CBM diagnosis mapping (this will be corrected soon) Preservation not mapped

Questions Questions before demo?