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1 A National Virtual Specimen Database for Early Cancer Detection June 26, 2003 Daniel Crichton NASA Jet Propulsion Laboratory Sean Kelly NASA Jet Propulsion.

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Presentation on theme: "1 A National Virtual Specimen Database for Early Cancer Detection June 26, 2003 Daniel Crichton NASA Jet Propulsion Laboratory Sean Kelly NASA Jet Propulsion."— Presentation transcript:

1 1 A National Virtual Specimen Database for Early Cancer Detection June 26, 2003 Daniel Crichton NASA Jet Propulsion Laboratory Sean Kelly NASA Jet Propulsion Laboratory Mark Thornquist Fred Hutchinson Cancer Research Center Sudhir Srivastava National Cancer Institute Heather Kincaid Fred Hutchinson Cancer Research Center Donald Johnsey National Cancer Institute Marcy Winget Fred Hutchinson Cancer Research Center

2 2 Vision Development of a world-wide knowledge and informatics environment for sharing cancer specimen data across repositories Data and Computers interconnected to form a virtual database Integrated Cancer Resources Specimens Images Assays Biomarkers etc

3 3 Early Detection Research Network (EDRN) w 5-Year collaboration supported by NCI w Goal: Identify, evaluate, and validate promising biomarkers to support the early detection of cancer w Comprised of: 18 Biomarker Laboratories 9 Clinical and Epidemiology Centers 3 Biomarker Validation Laboratories Data Management and Coordinating Center

4 4 EDRN Resource Network Exchange (ERNE) w Virtual Specimen Repository (real-time access to distributed repositories) w Informatics infrastructure created for EDRN w Existing sites specimen databases maintained locally w Uses EDRN Common Data Elements (CDEs) w Maps institutions local data definitions to EDRN CDEs w Secure and Confidential w Secure Dynamic Portal

5 5 Informatics Deployment

6 6 Information Infrastructure Progress Initiation (10/00 - 3/01) Connect Moffitt and San Antonio Finalize EDRN CDEs used in knowledge system Create Dynamic Portal Present Feasibility at EDRN S.C. Meeting Discuss Informatics at 2 nd EDRN S.C. Meeting Present Mock Knowledge System at EDRN S.C. Meeting Feasibility (4/01 - 10/01) Pilot (10/01 - 9/02) Implement four sites Finalize IRB Protocol template Create Online Mapping Tool Present at EDRN S.C. Meeting Implementation (9/02 - 6/03) Implement three additional sites Present at EDRN S.C. Meeting

7 7 EDRN Bioinformatics Architecture 3. Repositories for storing and retrieving many data types data 1. Bioformatics tools and applications use “API” Visualization Tools Analysis Tools “OODT” Middleware “OODT” Middleware EDRN Data Repositories EDRN Data Repositories API 2. Middleware creates the informatics infrastructure connecting systems and data SPORE Data Repositories SPORE Data Repositories Other Data Repositories Other Data Repositories API Web Search Tools Metadata Mediation Standard Metadata

8 8 Informatics Infrastructure w Connect local databases via the Internet w Query multiple institutional databases concurrently w Metadata-based distributed framework w Object Oriented Data Technology (OODT) framework (JPL) Combines semantic data model with distributed services to create a “grid” architecture

9 9 OODT Framework w Developed by NASA to support science data management for the robotic planetary program w Defines a reusable architectural pattern that enables information clustering and retrieval across distributed data resources intelligent query algorithm for scalability interoperability between disparate data models a reusable software components domain independence plug-in for various distributed computing implementations

10 10 Critical OODT Components w Query Server – Manages and routes concurrent queries to distributed resources. Combines results. w Profile Server – Enables resource discovery providing information about what data resources are available (a resource is really an electronic object) w Product Server – Enables access and retrieval of data products from an online data source w Servers written in Java and supported on Windows, Linux, Solaris, Mac OS X, etc

11 11 Software Component Deployment User query EDRN Secure Website QueryClientWeb server search.jsp Product Server Moffitt EDRN Profile Server EDRN CDE Mapping Database Specimen Database Specimen Database Specimen Database Specimen Database Specimen Database Specimen Database DMCC – Fred Hutchinson Cancer Research Center Science Tools User query Specimen Database Specimen Database Product Server San Antonio Product Server MD Anderson Product Server Colorado Product Server Creighton Product Server GLNE Product Server Pittsburgh Product Server New York Product Server Brigham and Womens Specimen Database

12 12 Semantic Architecture w Define a common data model for EDRN Common Data Elements Relationships between elements w Institutions have existing specimen repositories with locally defined data models Map local data elements to CDEs using EDRN CDE mapping and repository tools 39 CDEs Shared w Use Standards ISO/IEC 11179 Resource Description Framework (RDF) w Use standard definitions for data exchange Communicate using a standard XML schema

13 13 Gender Mapping Example

14 14 Security and Confidentiality w Highly Sensitive Information w Health Insurance Portability and Accountability Act (HIPAA) Removed Personal Health Information (PHI) w Security Measures 128-bit strong encryption using Secure Socket Layer (SSL) Access limited to remote connect from specific IP(s) on specific ports. Firewalls augmented with rule set. w Institutions IRBs Common Protocol

15 15 Dynamic Portal

16 16 Advanced Search

17 17 Results

18 18 Number of Participants by Specimen Type

19 19 ERNE Achievements w Deployed Software Infrastructure to 10 institutions Process of connecting new sites well understood w Software Infrastructure Maturing Extensive nightly testing and monitoring of infrastructure w Team Maturing and Growing w Policy Challenges w Institutional Access w Science Support

20 20 More Information w EDRN – http://www.cancer.gov/edrnhttp://www.cancer.gov/edrn w OODT – http://www.jpl.nasa.govhttp://www.jpl.nasa.gov w Contact: Heather Kincaid: hkincaid@fhcrc.orghkincaid@fhcrc.org Dan Crichton: Dan.Crichton@jpl.nasa.govDan.Crichton@jpl.nasa.gov Don Johnsey: johnseyd@mail.nih.govjohnseyd@mail.nih.gov

21 21 Quick Search

22 22 Dynamic Portal w JSP-based implementation that queries informatics infrastructure Uses CDE terms for constructing query expression w Shows available servers w Limit available choices based on selected criteria w Quick Search w Advanced Search

23 23 Quick Search Results

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