Integrated Data Management System for the Biorepository.

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 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

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 Registry

CDW

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