Implementing Biospecimen Management and Data Federation Technologies to Support the UHN Research Community

Transcription

1 Implementing Biospecimen Management and Data Federation Technologies to Support the UHN Research Community T. Michaelson IT Development Team Leader Biospecimen Management Technologies and Data Federation UHN/TECHNA December 4, 2014

2 Acknowledgements Heather Begley Gavin Disney Nazish Qazi Patricia Li Paul Homer Dr. D. Jaffray Dr. C. Paige Dr. M. Roehrl Dr. D. Chadwick Research Information Systems (RIS) UHN Shared Information Management Services (SIMS) Radiation Medicine Program eservices

3 Funded by a CFI grant Project Genesis Biospecimen Management and related Clinical Annotation was one theme among many in this grant Signal Transduction and Disease-B. Neel Image guided discovery in Health and Disease-D. Jaffray Biomarker Discovery-E. Fish Clinical Studies Platform-C. Bombardier Stem Cells and Tissue Engineering-G. Keller Immunity in Health and Disease-P. Ohashi Drug Discovery and Development-E. Pai, B. Greenberg

4 Project Description Deploy a robust, centralised UHN Biospecimen Management System Deploy a robust standardised Clinical Annotation Tool linked to the Biospecimen Management System Federate data with other UHN databases Integrate legacy data where practical Federate data dynamically where possible Persist federated data where necessary Align with UHN ACD and CDR projects Align with UHN s desire to be the Research Hospital of the Future

5 Principles Broad Focus (cancer and non-cancer research) Flexible Federated Data Model Utilize Open Source Software where possible Leverage Existing Infrastructure Minimize data transcription and duplicate data entry Capitalize on Existing Development Skill-Sets Ongoing Operational & Research Commitment

6 Implementation Phases Caisis-Clinical Annotation catissue Suite-Biospecimen Mgmt. Phase 1 Phase 2 Phase 3 catissuesuite General Biospecimen Mgmt Caisis Biospecimen Clinical Annotation Reporting and Analysis Data feeds from NODR and CoPath Implementation of disease sites (Cancer and non-cancer) Federate Data Sources Federated system deployed Handoff to Operations Group

7 Primary Software Tools- Open Source CaTissueSuite/Open Specimen Biospecimen Management System Originally part of the cabig initiative Software renamed Open Specimen Caisis Clinical Annotation System Developed at Memorial Sloan-Kettering Contains Pathology and other clinical data captured from source systems or data entered by the user Features Web based Handles oncology and non-oncology datasets and specimens Global Community of Support No Ongoing Licensing Fees

8 Data Federation Def: The process of bringing data together in a single virtual location for on-demand application access.

9 Data Federation Tool SAP Business Intelligence Robust data federation functionality Aggregate data across multiple data sources Data cleansing and parsing Web-based interface and privilege-based access Data visualisation via Dashboards and Reports Federated data can be exported to a research analysis tool (Biomart, SAS etc.) Software licensing required

10 Biobanking Technologies IT Development Team Small, Nimble, Focused Team 3.5 FTE Programmers-Bootstrap 2.1 FTE Programmers-Ongoing Substantial Biospecimen Management Expertise Excellent Programming and Configuration Skills.5 FTE Project Team Leader/Manager-Bootstrap.2 FTE Project Team Leader/Manager-Ongoing Experience and success with large and complex systems implementations

11 The Biospecimen Technologies Team collaborates with SIMS, RIS and Pathology to establish and maintain the necessary interfaces critical the success of the project ADT info from EPR via NODR Lab results and visit info from EPR via NODR Pathology Reports (Synoptic and Full Text) from Copath Future Interfaces and Federations with UHN systems

12 Current state of the Project Current Implementations UHN Biobank (All Technologies) PM Cancer Registry (Federation Only) UHN Cardiac Program (Federation Only) Undergoing Implementation PM GU Bank PM Leukemia Program UHN Orthopaedics Program Toronto Brain Bank Implementation Discovery Underway UHN Liver Transplant UHN Bone Marrow Transplant Others

13 Initiation Process A Program makes contact or is referred to the Biobanking and Data Federation Technologies Team (BDTF) A meeting arranged and a discovery process initiated If there is agreement to go forward after the discovery process, a Statement of Work (SOW) is created and agreed to by the Program and the BDTF The SOW includes tasks, timeline estimates, and costs

14 Federation and Reporting Example User logs into a secure web portal Enters search criteria Returned results are dependent on the level of access granted to the users (e.g. scope of REB approval) Access to all systems and data included in the federation is permission based Permissions are granular to the field level Governance policies control who can access data in a particular system within the federation

15 Example: Federated Reports via SAP

16 SAP Federated Dashboard

17 Slide Courtesy Dr. Michael Roehrl Research Informatics: Live Pathology

18 Slide Courtesy Dr. Michael Roehrl Connection: Personalized Deep Molecular Profiling

19 CoPath UHN Pathology Synoptic Reports UHN Research/TECHNA Biobanking and Data Federation Clinical Trials Caisis Clinical Annotations UHN EPR Patient Demographic Info SAP Data Federation and Reporting catissuesuite Specimen Management ecare DADOS PM Cancer Registry Clinical Annotation UHN Biobank Bloods and Body Fluids UHN Biobank Solid Tissue UHN Sites and Biobanks Leukemia G. U. Cancer Registry Orthopaedics Multi-Organ Transplant Liver Transplant Toronto Brain Bank Cell Therapy Head and Neck Cardiac Program Rheumatology Lymphoma Ovarian.others UHN Advanced Clinical Documentation Research Community External Sites CAMH Ontario Health Study ICES...others

20 Implementing Biospecimen Management and Data Federation Technologies to Support the UHN Research Community Thank You Questions?