# Presentation: 523524

## Informatics Pilot ProjectEDRN Knowledge System Working Group San Antonio, TexasJanuary 21, 2001

- Steve Hughes
- Thuy Tran
- Dan Crichton
- Jet Propulsion Laboratory, California Institute of Technology,
- National Aeronautics and Space Administration

## Problem Definition and Proposal

- Overview
- Problem: *Specimen data is geographically distributed across heterogeneous data systems making the location, retrieval and use of this data difficult.*
- Solution: Build a “data architecture” for the EDRN network
- Use “metadata” as a key to interoperability
- Provide services for data sharing, archiving and distribution
- Provide a software framework that allows analysis tools to be plugged into the EDRN data enterprise
- Benefit: Correlating data across multiple centers affords an opportunity to create new data sets and data awareness
- Example: Find all prostate tissue samples for men ages 70 and older collected before 1980 from databases across the EDRN

## EDRN Data Architecture Evolution

- Data System Evolution

- _Local Database_
-  - Local Tools
-  - No Data Sharing between
-    Centers
-  - No Common Data Elements

- _Limited Data Sharing_
-    - Manual Data Sharing
-    - Manual Correlation
-    - Export/Import Data
-    - Limited CDEs

- _Full Data Sharing_
-    - Location Independence
-    - Data Interchange
-    - Data Sharing
-    - Common CDEs between centers
-    - Heterogeneous Systems

*Locally Centralized Data*

*Interoperable & Distributed Databases*

## Completed Steps for the Mockup Implementation

- Extracted Data from Partner Centers
- Moffitt and San Antonio provided sample data sets to the DMCC and JPL
- Used “synthesized” data in lieu of “sensitive” data
- Preserved the original data structures provided by the centers
- Mapped Data Dictionary Terms
- Mapped common models between the EDRN CDE, Moffitt and San Antonio for correlating data sets
- Developed “Profiles” that represent data resources for San Antonio, Moffitt, DMCC, EDRN and NCI
- Hosted data and metadata “profiles” at JPL
- Integrated with an existing data sharing software framework developed by JPL called “OODT” or Object Oriented Data Technology
- Framework developed to share space science datasets across NASA’s distributed Planetary Data System
- Built a user interface to demonstrate a use case scenario for interoperability and data sharing between the databases

## Goals for the Mockup Implementation

- Demonstrate the Return on Investment (ROI) achieved in “federating” (or linking) laboratory data systems together
- Identify a scenario that demonstrates usability such as providing generic support for specimen data location and retrieval
- Use metadata (or *profiles*)
- “Recipes” to describe what data (specimen) and resources are available
- Communicate across systems
- Adoption of EDRN CDEs
- Look for common models between systems
- Understand how to relate center-specific metadata models
- Look for “low hanging” fruit
- Centers with similar databases and data models

## EDRN Knowledge ArchitectureMockup Implementation at JPL

***EDRN Knowledge Architecture******Mockup Implementation at JPL***

**EDRN Mock Databases **
**Hosted at JPL **

- In:Query
- Out::Identified Resources

- In:Query
- Out::Data Products

- In:Query
- Out::Data Products

**OODT**
**Middleware: **
**Hosted at JPL**

## Profile CDE Integration

- Describe specimen data, data servers, and other resources using metadata “profiles”
- Use Common Data Element (CDE) set for specimen description and search attributes
- Use industry standard metadata terminology such as Dublin Core
- Example Metadata Profiles:
- Mockup EDRN H. Lee Moffitt Cancer Center Product Server
- Mockup EDRN University of Texas, San Antonio Product Server
- Mockup EDRN DMCC Fred Hutchinson Cancer Research Center Query Interface
- Mockup EDRN DMCC Fred Hutchinson Cancer Research Center Web Site
- Early Detection Research Network Web Site
- EDRN Data Management and Coordinating Center Data Dictionary

## Data Element Comparison Chart

- *  As of 12/5/2000

## User Interface

- Provide a user interface to support various queries of related to cancer specimen data (_[http://](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[oodt](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[.](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[jpl](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[.](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[nasa](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[.](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[gov](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[/EDRN/search.](http://oodt.jpl.nasa.gov/EDRN/search.jsp)__[jsp](http://oodt.jpl.nasa.gov/EDRN/search.jsp)_ ):
- Find all prostate tissue samples for all men collected from San Antonio and Moffitt databases
- Find all prostate tissue samples for men ages 70 and older collected before 1980 from San Antonio and Moffitt databases sorted by Grade, Age, and Site
- Find all breast tissue samples from women ages 50 and older from San Antonio* and Moffitt databases
- Find all lung tissue samples from San Antonio and Moffitt databases *
- * San Antonio database contains just prostate

## Key Challenges

- Local data dictionaries and associated data models
- Different terms, data types, enumerated values, etc
- Different meanings and interpretations
- Different database product implementations
- Filemaker Pro and Microsoft Access
- Maintain the structural integrity of the data models
- EDRN CDEs exist for demographic data, but not  specimen data*
- JPL developed common CDEs between the two databases for the specimen data
- * As of 12/5/2000

## Next Steps

- Focus the implementation of data sharing on defining a robust metadata infrastructure
- Complete the EDRN CDE effort and begin a process of mapping the CDEs to the center databases
- Reuse this mockup experience as an example!
- Incorporate feedback from mockup presentation
- Address IRB and security requirements related to data sharing
- Encrypted and de-identified keys
- Network and computer security access
- Connect to databases physically located at the centers
- Implement data system interfaces to the remote databases

## Acknowledgements

- Lynn Anderson, H. Lee Moffitt Cancer Center
- Betsy Higgins,  University of Texas, San Antonio
- Heather Kincaid, Data Management and Coordinating Center, Fred Hutchinson Cancer Research Center
- Mark Thornquist, Data Management and Coordinating Center, Fred Hutchinson Cancer Research Center
- Ziding Feng, Data Management and Coordinating Center, Fred Hutchinson Cancer Research Center
- Greg Downing, Office of Science Policy, Office of the Director, National Institute of Health
- Sudhir Srivastava, National Cancer Institute

## Backup Slides

## EDRN Mockup Query Example

## EDRN Mockup Results – Query 1

## EDRN Mockup Results – Query 3

## EDRN Mockup Results – Query 4

## Detailed Search of Profiles

## Profiles of EDRN Resources

***Resource Profiles***

***EDRN***
***Resources***

## EDRN Mockup Data Flow

- Query Server

- Profile Serverjpl.edrn

- Product Serveredrn.moffitt

- Product Serveredrn.sanantonio

- Userquery

- XSL(profiles ordata productsformatted)

- XMLQuery/IIOP(no results)

- XMLQuery/IIOP(profiles ordata resultsas requested)

- XMLQuery/IIOP(no results)

- XMLQuery/IIOP(profiles of resources to handle query)

- XMLQuery/IIOP (data results)

- XMLQuery/IIOP (product search)

**Search Web Page**

**Profile DB**

**Moffitt “Mock” Database**

**San Antonio**
**“****Mock” Database**

- QueryClient

- Web server

- search.jsp

- Web
- EDRN/NCI
- Resources