Biorepository Software Selection University of Michigan 31-Aug-2012
Integrated Data Management System for the Biorepository.
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Transcript of Integrated Data Management System for the Biorepository.
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Integrated Data Management System
for the Biorepository
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Biorepository
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Part of the Mission and Goals Statement
… the limited availability of carefully collected andcontrolled, high-quality human biospecimens annotated
with essential clinical data and properly consented forbroad investigational use … is repeatedly identified by
the scientific community as a leading obstacle toprogress in post-genomics cancer research …
National Cancer Institute (NCI)Office of Biorepositories and Biospecimen Research (OBBR)
http://biospecimens.cancer.gov/about/overview.aspAccessed April 4, 2014
From the Office of Biorepositories and Biospecimen Research
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Standard Process
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Goal
• Combine different biobanks– Hollings Cancer Center– MUSC Brain Bank– SCTR biobank
• Link different data sets on one screen
For Researchers
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Goal
• Add additional knowledge relating to their samples without having to go to many different systems.
For Biorepository Personnel
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User Interface Capabilities
• 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
Admin Slide
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Background
• 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
Combines data from multiple data sources
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Technology Details
• 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
Geek Slide
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Identify System.
Can we Transform
Data Internally?
Does it have a Web
Service?
Staging Area
Application Web Service
START
YES
YES
NO
NO
Very Basic
Workflow
Data Access
Process
Transformas
needed
Balancing Act
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Biorepository Data
• 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
TissueMetrix using Oracle
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Storefront
Disease Sites Cases Tumor Primary
Plasma Buffy Coat Plasma
Anal
Bladder
Breast
5
256
190
9
451
365
20
700
250
10
277
292
TissueMetrix data
19
233
345
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Creating a Worksheet
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Shopping Cart List
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CDW
• 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
Clinical Data Warehouse using Sybase IQ
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Cancer Registry
• Web Service to access data• Pass in an MRN and get back– Tumor Information– Histology– Grade– Treatment– Other areas
Commercial Program using MS SQL
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Path Reports
• 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
Cerner CoPathPlus streaming HL7 messages
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So what did we end up with
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TBDSources
Radiology Cancer Registry
CDW
Path Reports TissueMetrix
Web Service
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End User
has a:
Larger set of
Data
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Rather
than:
Or stumbling
around in the
dark
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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
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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
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What have we learned
Think outside the
box
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Before the DemoAny Questions?
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Contact Information
Anita L. Harrison, MPAAssociate Director of AdministrationHollings Cancer CenterMedical University of South Carolina
William [email protected]
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