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Integrated Data Management System

Integrated Data Management System. for the Biorepository. Biorepository. From the Office of Biorepositories and Biospecimen Research. Part of the Mission and Goals Statement. … the limited availability of carefully collected and controlled, high-quality human biospecimens annotated

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Integrated Data Management System

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  1. Integrated Data Management System for the Biorepository

  2. Biorepository

  3. From the Office of Biorepositories and Biospecimen Research Part of the Mission and Goals Statement … the limited availability of carefully collected and controlled, high-quality human biospecimens annotated with essential clinical data and properly consented for broad investigational use … is repeatedly identified by the scientific community as a leading obstacle to progress in post-genomics cancer research … National Cancer Institute (NCI) Office of Biorepositories and Biospecimen Research (OBBR) http://biospecimens.cancer.gov/about/overview.asp Accessed April 4, 2014

  4. Standard Process

  5. Goal For Researchers • Combine different biobanks • Hollings Cancer Center • MUSC Brain Bank • SCTR biobank • Link different data sets on one screen

  6. Goal For Biorepository Personnel • Add additional knowledge relating to their samples without having to go to many different systems.

  7. User Interface Capabilities Admin Slide • Filter by ICD-9 codes – diagnostic descriptions • Filter by demographics • Age • Sex • Race • Ability to de-identify data or eliminate entirely • Maintain an audit trail of samples reviewed • Add to shopping cart or wish list • Simple to use

  8. Background Combines data from multiple data sources • Campus wide use of TissueMetrix using Oracle • Clinical Data Warehouse using Sybase IQ • Cancer Registry’s IMPAC system using MS SQL • Cerner CoPathPlus streaming HL7 messages • PenRad for mammography informatics • Lucene.Net indexing ICD-9 codes • Excel spreadsheets

  9. Technology Details Geek Slide • Portal uses DNN as foundation • Authentication using LDAP • ICD-9 searches are created using Lucene.net • User Interface uses HTML5, JavaScript, jQuery • Web Services are written in JSON • MS SQL is used for middle tier • 128 bit Encrypted values change every 3 minutes

  10. START Very Basic Workflow Data Access Process Identify System. Can we Transform Data Internally? NO YES Staging Area Does it have a Web Service? NO Transform as needed YES Application Web Service BalancingAct

  11. Biorepository Data TissueMetrix using Oracle • Export data nightly to MS SQL database Data Warehouse • Data is transformed and cleansed so it has consistent meaning. • May involve restructuring, redefining, filtering, combining, recalculating and summarizing data fields

  12. Storefront TissueMetrix data Tumor Primary Buffy Coat Plasma Disease Sites Cases Plasma 19 20 10 9 5 Anal 233 700 277 451 Bladder 256 345 250 292 365 Breast 190

  13. Creating a Worksheet

  14. Shopping Cart List

  15. CDW Clinical Data Warehouse using Sybase IQ • Web Service to access data • Pass in an MRN and Date Range get back ICD-9 Codes • Working on: • Getting back Lab results • Getting back Treatments • Other areas

  16. Cancer Registry Commercial Program using MS SQL • Web Service to access data • Pass in an MRN and get back • Tumor Information • Histology • Grade • Treatment • Other areas

  17. Path Reports Cerner CoPathPlus streaming HL7 messages • HermeTech HL7 listener • De-identifying Message and build the document based upon the role of the user. • Pass the data down in JSON to be displayed as standard HTML

  18. So what did we end up with

  19. Path Reports TissueMetrix Web Service CDW Radiology Cancer Registry TBD Sources

  20. End User has a: Larger set of Data

  21. Rather than: Or stumbling around in the dark

  22. Security • 128 bit Encrypted value changes every 3 minutes and is included in the Header of every browser request • MRN is passed encrypted with key that changes every 3 minutes • Values are checked on the Web Server to be within accepted values before sending to the Database Server

  23. Summary • Provides researchers with a simplified view of specimens in inventory • Users do not require direct access to the database • Provides for electronic messaging when further interest in specimens is identified • Identifies availability of specimens for grant proposals

  24. What have we learned Think outside the box

  25. Before the DemoAny Questions?

  26. Contact Information • Anita L. Harrison, MPA • Associate Director of Administration • Hollings Cancer Center • Medical University of South Carolina • William Morgenweck • morgenww@musc.edu • Storefront

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