Transcript OnCore at VCU

Informatics Tools and Services
Biomedical Informatics Core
Tim Aro
Informatics Tools and Services
CCTR Biomedical Informatics Core
Electronic Data Capture (e.g. REDCap)
Cohort Discovery (i2b2 and new initiatives)
Data Extracts – EMR (Cerner) and Billing System (IDX)
Clinical Trial Management System (CTMS) support and training (OnCore)
Research Collaboration Environment (Research Portal)
Researcher Networking (VIVO)
Honest Broker Services
Research Subject Recruitment
Bioinformatics Tools/Services
redcap.vcu.edu
Secure Web-based Database and Surveys
Customizable – Intuitive UI or Data Dictionary
Multi-site Studies – Data Access Groups
Access Controls – User Rights
Robust Intuitive Reports and Data Exports
IRB Approved - Recommended
Free to VCU/VCUHS Faculty, Staff, Students, Affiliates
i2b2
informatics for integrating biology & the bedside
Developed at Harvard Partners Healthcare through a CTSA grant, i2b2 is a query tool
that allows uses to search selected clinical and billing data from VCU Health.
Cohort identification – Users may search a de-identified database, without IRB
approval, to determine the existence of a set of patients meeting specified criteria.
The data are presented as unique patient counts. This means a patient is counted
exactly once if he/she ever met the criteria specified by the query.
SHRINE*
Shared Health Research Informatics NEtwork
i2b2 SHRINE allows institutions to share data while protecting patient privacy and
providing researchers access to large sample sizes not easily available at any single
institution.
VCU / PSU Collaboration
We are currently working towards sharing the following data between institutions:
• Demographics
• Visit Type
• Diagnosis codes (ICD-9)
* Labs, Medications (future state)
Use Case: Crohn’s Disease - Penn State PhD candidate
*Initiative in progress – Fall 2016 projected go-live
TriNetX*
TriNetX is a federated clinical data network of providers and
pharmaceutical companies used to enhance clinical trial design
and accelerate trial site and patient recruitment.
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Patient Recruitment made easier
Better understand the target patient population
Potential Sponsorship from pharmaceutical companies
May Collaborate with other TriNetX members
*Initiative in progress - Winter 2017 projected go-live
Need Data?
Conduct a Simple Chart Review in Cerner
e.g. Find data on 500 potential subjects (just look ‘em up!)
Data Extraction
CCTR Biomedical Informatics Core
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BIC data request form is submitted (go.vcu.edu/bicrequest)
Analyst meets with researcher
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Analyst researches source systems to find the appropriate data
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Discuss overall project goals
Review requested data elements
Gather screen shots of requested data in source front-end
Collect sample MRNs that have requested data
Cerner Millennium EMR
GE Centricity (formerly IDX) Billing
Philips OB TraceVue
Other VCU or VCU Health System source systems
Merge data provided by researcher and disparate sources
Deliver identified or de-identified data extract to researcher
Data Extraction Use Case: HCV Target
CCTR Biomedical Informatics Core – Data Extract Use Case
University of North Carolina
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Internet
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Generate_subject_mapper_input.py(script1
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Output from script: smi.xml
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UFL PUTS smi.xml on BIC
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University of Florida
Cron runs
generate_subject_map.py(script2)
every 24hr
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API
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Output.csv
SFG PUTS VCUHCV.csv
Generate_subject_map
utilizes REDCap API
Research portal (SFTP)
(research portal)
VCU REDCap
SFG GETS output.csv from BIC FTP
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Sterling File Gateway (VCUHS)
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DATA-STAGE generates
VCUHCV.csv
DATA-STAGE GETS
8 subject_data.csv from SFG
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Oracle
(DSSDWPARS1)
DATA-STAGE creates Oracle table,
HCV_SUBJECT_DATA, on
DSSDWPARS1.BIC
DATA-STAGE
OnCore at VCU – Enterprise Wide CTMS
Learn More About OnCore at VCU
Robert B. Moulden
OnCore CTMS Manager
[email protected]
Mary M. O'Connell
OnCore Trainer
[email protected]
Research Portal – Collaboration Environment
go.vcu.edu/bicportal
VIVO - communitynetwork.vcu.edu
Honest Broker Services
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Collaboration with the Cancer Informatics Core
IRB approved Honest Broker Protocol
PI is Tamas Gal, PhD
Provide De-Identified data – with surrogate IDs
Clinical Trial Recruitment Tools
StudyFinder.cctr.vcu.edu
Mobile App
Bioinformatics Tools and Services
Making sense of the massive amounts of genomic data can be a
daunting task. Bioinformatics utilizes computational tools to
organize, analyze and store such data generated by the life
sciences and health industry. The CCTR offers a range of
bioinformatics and related services:
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Bioinformatics I and Bioinformatics II short courses
Free consultations
Assistance on project management and experimental design
Grant/proposal and manuscript writing
Data analysis, visualization and interpretation
Long-term research support for funded grants
Need Help?
Request Informatics Services
go.vcu.edu/bicrequest
Team Members
Directors
Dr. Krys Cios and Dr. Jon DeShazo
Key Individuals
Shannon Bruffy - i2b2 Analyst
Jun He - Oncore Administrator/Data Analyst
Mike Tran – REDCap Administrator/Developer
Sowmya Nadiminti – Infrastructure Analyst
Brian Bush – Special Projects – IT Analyst
Patrick Shi – REDCap Support Technician
Bobby Moulden – OnCore Manager
Amy Olex – Bioinformatics
Tamas Gal – Cancer Informatics Core
Mike Sarkissian – Enterprise Data Warehouse Architect
CCTR Informatics Tools and Services
Important Links (w/login info)
Request Assistance
go.vcu.edu/bicrequest (no login)
Tools
REDCap: redcap.vcu.edu (eID)
I2b2:
go.vcu.edu/i2b2 (account needed)
Portal:
go.vcu.edu/bicportal (eID)
Experts: communitynetwork.vcu.edu (no login)
Recruit:
studyfinder.cctr.vcu.edu (no login)
http://cctr.vcu.edu/informatics/biomedical/index.html