Overview of the Integrated Postsecondary Education Data System (IPEDS)
Integrated Data Management System
description
Transcript of Integrated Data Management System
Integrated Data Management System
for the Biorepository
Biorepository
Part of the Mission and Goals Statement
… the limited availability of carefully collected andcontrolled, high-quality human biospecimens annotatedwith 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
Standard Process
Goal
• Combine different biobanks– Hollings Cancer Center– MUSC Brain Bank– SCTR biobank
• Link different data sets on one screen
For Researchers
Goal
• Add additional knowledge relating to their samples without having to go to many different systems.
For Biorepository Personnel
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
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
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
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
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
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
Creating a Worksheet
Shopping Cart List
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
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
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
So what did we end up with
TBDSources Radiology Cancer
RegistryCDW
Path Reports TissueMetrix
Web Service
End User
has a:
Larger set of
Data
Rather than:
Or stumbling
around in the
dark
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
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
What have we learned
Think outside the
box
Before the DemoAny Questions?
Contact Information
Anita L. Harrison, MPAAssociate Director of AdministrationHollings Cancer CenterMedical University of South Carolina
William [email protected]
Storefront