Translational Informatics
@ UCSF
1nf0rmatics Day
June 10th
, 2014
Sorena Nadaf M.S.,M.MI
Associate Director HDFCCC
Chief I...
“Science is evolving at an incredible pace.
It’s a revolutionary period. The fundamental
change is that biomedical science...
3
• The landscape of clinical, basic science, and
translational research has evolved and is still rapidly
changing
• Enabl...
TIME
UNDERSTANDING
OF DISEASES
TRANSLATIONAL
RESEARCH
MANAGEMENT
OF
PATIENTS
INFORMATION Accelerating Personalization of C...
• Bridge the lab and clinic in both directions
• Accelerate development of individual targeted agents
Small molecules
An...
• Integration of Genomics, Molecular Diagnostics and Therapeutics
• Collaboration of Multiple Groups
•Academia, NIH/NCI, F...
Landscape: “…multiple collaborating investigators working
as an investigative team in order to address complex
biomedical ...
Mission
Deliver Suite of Services to support translational,
biomedical, and clinical research, as well as clinical care
im...
• Identify and prioritize informatics needs in consultation
with Faculty and Staff
• Evaluate alternative software and som...
• Provide consultation to facilitate use of specialized
database software and bioinformatics tools
• Develop and implement...
•Provide Data Consultation and Research Design
•Clinical / Biomedical Research Infrastructure
•Clinical Research Informati...
1212
Centralized Research Data Management & Coordination
TITI
Program
Support
Services
Quality
Control
Integration
Adoptio...
• Infrastructure : Data Coordinating Center
• Clinical Research Informatics: Robust Clinical Data Capture &
Trials Managem...
• OnCore Help-Desk
• Facilitate, Centralize, and Standardize Clinical Trial
Research Data Collection
• Example: Completion...
 Total Protocols : 4171
 Total Active Protocols : 1682
 Total Protocol Documents : 31,695
 Total SAE’s : 2646
 Total ...
• Phase I : HL7 Live Data Feeds
• APeX Patient Demographics
• APeX LABS
• Phase II:
• APeX RPE,
• APeX Billing Grid
Demographics (HL7 ADT: APeX > OnCore)
Push subject demographics information from EMR
Laboratory (HL7 ORU: APeX > OnCore)
P...
Patient Demographics (Completed)
 Fundamental Building Block of Integration
 APeX Pushing Patient Demographic Data: i.e....
Additional Interoperability Projects
• CHR’s iRIS iMedRIS
 Phase I :
o iRIS > OnCore (in Progress)
o iRIS Reporting via i...
Natural Language Processing: From Text to Meaning
21
Transform Text into Insights
Turn text
Into structured data
using sophisticated queries
To drive
analytics
APeX
Cancer
Reg...
Discussion
UCSF Informatics Day 2014 - Sorena Nadaf, "Translational Informatics OnCore Clinical Research and Integration with APeX an...
UCSF Informatics Day 2014 - Sorena Nadaf, "Translational Informatics OnCore Clinical Research and Integration with APeX an...
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UCSF Informatics Day 2014 - Sorena Nadaf, "Translational Informatics OnCore Clinical Research and Integration with APeX and iRIS"

Published on: Mar 3, 2016
Published in: Science      Health & Medicine      Business      
Source: www.slideshare.net


Transcripts - UCSF Informatics Day 2014 - Sorena Nadaf, "Translational Informatics OnCore Clinical Research and Integration with APeX and iRIS"

  • 1. Translational Informatics @ UCSF 1nf0rmatics Day June 10th , 2014 Sorena Nadaf M.S.,M.MI Associate Director HDFCCC Chief Informatics Officer, Director of Translational Informatics Program
  • 2. “Science is evolving at an incredible pace. It’s a revolutionary period. The fundamental change is that biomedical science has converged… Elias Zerhouni, M.D. 2
  • 3. 3 • The landscape of clinical, basic science, and translational research has evolved and is still rapidly changing • Enabled by: • Genomics, High Throughput Molecular Science • Ubiquitous data communications & computing • Driven by National Programs: • Precision Medicine and Knowledge Networks • NIH / NCI Roadmaps • Translational & Biomarker Discovery Programs like SPORE’s and SPECS • BD2K
  • 4. TIME UNDERSTANDING OF DISEASES TRANSLATIONAL RESEARCH MANAGEMENT OF PATIENTS INFORMATION Accelerating Personalization of Care Challenge: Filling in the Gap
  • 5. • Bridge the lab and clinic in both directions • Accelerate development of individual targeted agents Small molecules Antibodies siRNAs • Accelerate development of individual biomarkers Risk Tumor Burden Predictive markers for response
  • 6. • Integration of Genomics, Molecular Diagnostics and Therapeutics • Collaboration of Multiple Groups •Academia, NIH/NCI, FDA, Pharma, Technology Partners • Establish Translational Support Teams and Infrastructure • Platform of common Informatics tools and Infrastructure • Standards – Its all about this – really ! • Sustained Architecture • Systems Interoperability and Data Integration
  • 7. Landscape: “…multiple collaborating investigators working as an investigative team in order to address complex biomedical science problems…” Leveraging Integrative Informatics Standards & Platforms to Enable High-throughput Translational Research Infrastructure for Collection, Management, Preservation, and Rapid Analysis of Clinical, Biomedical, and Biospecimen data under compliant conditions
  • 8. Mission Deliver Suite of Services to support translational, biomedical, and clinical research, as well as clinical care improvement. Focus Development of Systems and Infrastructure for the - Capture, Storage, Dissemination of Clinical, Biomedical, and Research Data that can easily be merged, integrated, or aggregated with other data sets. - Integration of unified technology platforms leveraging cutting-edge advances in Informatics and computing.
  • 9. • Identify and prioritize informatics needs in consultation with Faculty and Staff • Evaluate alternative software and sometimes hardware approaches and implement the selected solutions, with the goal of building an advanced integrated informatics environment • Assure compliance with governance, quality control, data privacy, and security standards for all informatics efforts. • Oversee adoption of related national policies, guidelines and standards for clinical and biomedical data / metadata
  • 10. • Provide consultation to facilitate use of specialized database software and bioinformatics tools • Develop and implement customized software and research databases • Data : Security, Compliance, Sharing, Governance • Relationship as appropriate with Vendor Community • Provide Biomedical Informatics systems and expertise in support of grants, projects, and the preparation of manuscripts
  • 11. •Provide Data Consultation and Research Design •Clinical / Biomedical Research Infrastructure •Clinical Research Informatics •Decision Support Service Infrastructure •Biospecimen / Tissue Informatics •Biomedical Informatics •High Performance Computing •Data Management and Integration •Data Marts & Data Mining •Informatics Education & Domain Expertise
  • 12. 1212 Centralized Research Data Management & Coordination TITI Program Support Services Quality Control Integration Adoption Quality Assurance Training
  • 13. • Infrastructure : Data Coordinating Center • Clinical Research Informatics: Robust Clinical Data Capture & Trials Management System: OnCore EDC and CTMS (Lindsey Watt Alami Presentation Later Today) • Clinical Registries (URM, REDCap) • Biospecimen Informatics (BSM, STARS, LabVantage*) • Patient Reported Outcomes (VissionTree) • Federated Electronic Data Marts • Business Intelligence Framework and Sophisticated Reporting • Integration and Interoperability : CHR iRIS, APeX, Radiology • NLP Methods and Tools • HPC and BIG Data : High Performance Compute Resource: TIPCC (Richard Johnston @ Genius Booth)
  • 14. • OnCore Help-Desk • Facilitate, Centralize, and Standardize Clinical Trial Research Data Collection • Example: Completion of Protocol Registration Form and submission • Example: Creating and Managing creation of all Patient Study Calendars and CRF’s • Reporting and Data Extraction and Integration • Study information portal linkage locally and for Public • Continued Training and Hands On Support • Continued Data Quality Control and Auditing
  • 15.  Total Protocols : 4171  Total Active Protocols : 1682  Total Protocol Documents : 31,695  Total SAE’s : 2646  Total Subjects : 28,028  Active Users: 923  Protocols added in last 12 months: 446  222 oncology  224 non-oncology *As of April 2014 – UCSF Wide
  • 16. • Phase I : HL7 Live Data Feeds • APeX Patient Demographics • APeX LABS • Phase II: • APeX RPE, • APeX Billing Grid
  • 17. Demographics (HL7 ADT: APeX > OnCore) Push subject demographics information from EMR Laboratory (HL7 ORU: APeX > OnCore) Populate OnCore eCRFs with lab results from lab system Protocol Setup (RPE) (OnCore > APeX) Sets Up Study Subjects in APeX: Information from OnCore is pushed to Epic to ‘flag’ subjects on a research study in OnCore: Protocol Billing Grid (OnCore > APeX) Provides an EMR with relative time points of a research study calendar including codes, billing designations and modifiers for assigned charge events & items. Purpose is to support billing compliance.
  • 18. Patient Demographics (Completed)  Fundamental Building Block of Integration  APeX Pushing Patient Demographic Data: i.e. • MRN • Name • Race • Ethnicity • Gender • Date of Birth • Address • Phone Number  Ensures the MRN from the EMR is the SAME primary research subject identifier: CRITICAL to the remaining, more advanced layers of integration
  • 19. Additional Interoperability Projects • CHR’s iRIS iMedRIS  Phase I : o iRIS > OnCore (in Progress) o iRIS Reporting via iMolytics Analytics  Phase II : OnCore > iRIS (under planning) • Radiology > OnCore (under planning) • KBase / PMP Project (under discussion) • VissionTree P.R.O (under discussion) • coPath Pathology Reports • coPath > OnCore BSM > Via i2e NLP Engine
  • 20. Natural Language Processing: From Text to Meaning 21
  • 21. Transform Text into Insights Turn text Into structured data using sophisticated queries To drive analytics APeX Cancer Registry OnCore Biobank
  • 22. Discussion

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