EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Douglas J. Buell Project Specialist Dana-Farber.

EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Douglas J. Buell Project Specialist Dana-Farber Cancer Institute Daniel Quinn System Programmer Dana-Farber Cancer Institute

Introductions Discussion Conclusion with Q&A Agenda Challenge Solution
Supporting tools Conclusion with Q&A

About Dana-Farber/Harvard Cancer Center
DF/HCC is the most extensive cancer research center in the world Founded in 1997 with a grant from the National Cancer Institute 900 Cancer Researchers [basic + clinical] Consortium of the 7 Harvard University affiliated institutions Research funding totaled $350 million in ‘06 In 2006: 689 accruing clinical trials 11,786 subjects accrued to clinical trials 204 active Principal Investigator Initiated (PII) clinical trials 3-4 new PII trials are activated each month For more InFormation

DF/HCC Member Institutions

Background BMT Volume: Over the last 15 years
100 protocols, 14 open ended standard treatment plans 4000 transplants Paper forms key punched into database Ingres (Legacy RDB)

5000 lines of legacy SAS code
Background cont’d Ingres 5000 lines of legacy SAS code Legacy Reporting Clinical Trial Research Operational/ Regulatory Reports National and International BMT registries Insurance companies Bio-Stats Analysis Administrative reporting

The Challenge Integration of old and new data
Ingres data Forms have changed over the years Many data points retired as forms changed 1 table = 1 form format InForm Trial Silos (trials are isolated from each other) Transactional DB is highly normalized data New form standards Data conversion out of the question InForm is a data collection tool, not a repository for legacy/static Different study versions would need to be developed to represent form changes over the 15 year span

More Challenges Consolidated Core study Company standards
60 forms 400 rules/contexts in InForm Company standards Naming conventions Inconsistent code list values Need for reusable forms Legacy Reporting requirements Crucial SAS reports to insurance providers, national and international agencies, and internal form/data management needed to be preserved Patient survival legacy data still needs to be reported Bone Marrow Transplantation has same regulatory requirements as solid organ transplants Access to data for Biostatistics

Oracle Based BMT Repository Mapping to match Ingres View
Our Solution Oracle Based BMT Repository InForm Trial InForm Trial Materialized View of Trial Materialized View of Trial Materialized View of Trial BMT Paper Trials InForm Trial InForm Trial InForm Trial BMT_Clinical View InForm Trial InForm Trial InForm Trial Mapping to match Ingres View InForm Trial InForm Trial Legacy Data View of Legacy Table (form) Final Reporting View (Materialized) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity SAS Report

Oracle Based BMT Repository
Our Solution Use SAS/Access to copy Ingres data to Oracle Oracle Based BMT Repository BMT Paper Trials Legacy Data View of Legacy Table (form) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity

SAS/ACCESS To Copy Ingres Tables To Repository
Create one LIBREF to Ingres, and one LIBREF to Oracle Initially use a DATA step to copy each Ingres table to Oracle, recreate integrity constraints on the Oracle copies Daily full comparison of Ingres tables to Oracle copies Daily PROC SQL DML statements on Oracle copies to synchronize

Oracle Based BMT Repository
Our Solution Access eDC data through Materialized Views in BMT Repository Oracle Based BMT Repository InForm Trial InForm Trial Materialized View of Trial Materialized View of Trial Materialized View of Trial BMT Paper Trials InForm Trial InForm Trial InForm Trial BMT_Clinical View InForm Trial InForm Trial InForm Trial InForm Trial InForm Trial Legacy Data View of Legacy Table (form) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity

Materialized Views to Copy Trial Data To Repository
Automatically create one materialized view for each trial via database procedure InForm numeric IDs are replaced with names, which are consistent across all trials and uniquely identify each data item Materialized views are refreshed through a database link

Materialized Views to Copy Trial Data To Repository
One Oracle SQL view combines all Trial views into a BMT_Clinical Data view Each Trial view is refreshed daily depending on activity in the InForm trial

Our Solution Mapping Repository Data into SAS ready Views Oracle Based BMT Repository InForm Trial InForm Trial Materialized View of Trial Materialized View of Trial Materialized View of Trial BMT Paper Trials InForm Trial InForm Trial InForm Trial BMT_Clinical View InForm Trial InForm Trial InForm Trial Mapping to match Ingres View InForm Trial InForm Trial Legacy Data View of Legacy Table (form) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity

Transform EDC Trial Data To Match Ingres Table Structures
A mapping table associates InForm question values to an Ingres table and column and defines any data conversions A SAS program reads the mapping table and creates a SQL file that will generate materialized views closely resembling the Ingres tables The generated SQL file is run on the repository database Secondary views of the materialized views are created to exactly match the Ingres table structures

Our Solution Combining Ingres and eDC data into final Reporting Views Oracle Based BMT Repository InForm Trial InForm Trial Materialized View of Trial Materialized View of Trial Materialized View of Trial BMT Paper Trials InForm Trial InForm Trial InForm Trial BMT_Clinical View InForm Trial InForm Trial InForm Trial Mapping to match Ingres View InForm Trial InForm Trial Legacy Data View of Legacy Table (form) Final Reporting View (Materialized) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity

The Final Reporting Views
The InForm views are combined with its counterpart Oracle/Ingres table giving us the final set of reporting views used for all reporting and analysis The final view names and column names exactly match the original Ingres tables so that existing SAS programs can be run against the Oracle repository instead of the Ingres database

Our Solution SAS Reporting Oracle Based BMT Repository InForm Trial InForm Trial Materialized View of Trial Materialized View of Trial Materialized View of Trial BMT Paper Trials InForm Trial InForm Trial InForm Trial BMT_Clinical View InForm Trial InForm Trial InForm Trial Mapping to match Ingres View InForm Trial InForm Trial Legacy Data View of Legacy Table (form) Final Reporting View (Materialized) BMT Repository Now Nightly automated subject registration Nightly feed from InForm Trials Nightly feed from Ingres Flexible structure Materialized views to support old reporting needs. Future Automated Change Management Automated ref-name integrity SAS Report

Supporting tools CLIMS (Code List Management System) Access database
Consistent code lists values (e.g. Disease Sites) InForm control and element names (refnames) Works with form generator through Excel macro

Supporting tools Form generator Excel based
Generates XML for forms from Excel form specification file Architect is used for cleanup only

Supporting tools Item Refname Generator Excel Based
Generates refnames following standard naming convention in the Excel form specification file Architect is used for cleanup only

Supporting tools Validation tool Excel based
Used by the Form Generator to validate specs prior to form generation

Supporting tools Documentation tool Excel based
Converts InForm source (XML) into specifications

Supporting tools Rule Generator (in development) Excel based
Generates rules and contexts from specifications

Supporting tools Summary
CLIMS Naming Convention database Form generator From XLS to XML Refname generator From item name to refname Validation tool Checks for naming Checks for ranges and code values Documentation tool From XML to XLS Rule Generator (future) Creates rules in XLS SAS/ACCESS Transports data from Ingres to repository Oracle SQL Builds views Mapping Table Mapping InForm to Legacy Ingres data

Acknowledgments Phase Forward Technical Support
Poornima Chalasani (eDC Developer) Melinda Flood (eDC Business Analyst) Dr. William Ho (BMT Medical Director) Dr. Haesook Kim (BMT Biostatistics) Theresa Kriejger (BMT Lead Clinical Coordinator) Marina Nillni (eDC Program Manager) Joan Sullivan (eDC/Integration Developer) Marina Varshavsky (Associate Director for Data Management) Lev Vernovsky (eDC Developer)

Conclusion Questions and answers

EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Thank you

EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Douglas J. Buell Project Specialist Dana-Farber.

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EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Douglas J. Buell Project Specialist Dana-Farber.

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Presentation on theme: "EDC at Dana-Farber/Harvard Cancer Center: Implementing InForm to Support a Bone Marrow Transplant Program Douglas J. Buell Project Specialist Dana-Farber."— Presentation transcript:

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