Custom applications to manage clinical research data

The Innovation Core can create custom applications to manage clinical research data. Features include:

• A web interface for quick browsing and entry of data
• Custom imports to bring spreadsheets into a structured and auditable format with security and regular backups built in
• Integration with other resources to pull in demographics, labs, and genomics data automatically
• Data pipelines in R or Python to perform analysis or build reports 

Web-based patient/participant interventions

We can develop applications to support participant interventions, either for recruitment, participant-reported outcomes, or other purposes.

These interventions provide participants with the tools to participate in your study either by collecting responses or sharing important details regarding the study. 

Research repositories and registries

The Innovation Core builds custom research repositories and registries. Benefits and options include:

• Access controls to ensure that only your team can log in, with roles and permissions controlling what each member can see and do.
• A source of truth for published results
• Insights into the study population through reports and exploration
• Population with data from the EHR and regular updates as new encounters occur in Epic

Details on working with the Innovation Core

Our team works in an agile development environment, collaborating closely with you to design the best solution for your project. We can provide an estimate to support your grant application, including longer term collaborations funded by FTE on a grant. 

Common features we consider for all projects

• User roles and permissions 
• Integrations with other systems, including FHIR applications
• User controlled managed content 
• Reporting functionality 
• HIPAA compliance and IRB expiration monitoring 

Advantages to working with us

• Hosting/Maintenance 
• Secure coding practices 
• Authentication/Security* 
• Auditing* 
• Expertise in navigating OHSU regulatory and security requirements

(*) required by OHSU 

OHSU's OMOP repository

The RDS leverages an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) repository to access extensive electronic health record notes for usage in Natural Language Processing (NLP) applications.  

The OMOP CDM is an open community data standard, designed to standardize the structure and content of observational data and to enable efficient analyses that can produce reliable evidence (OHDSI.org).

Recent enhancements to the OHSU OMOP repository have included augmenting the data with demographic data (REALD) and other valuable data sets. We are in the process of implementing software tools to allow access to the data, perform analysis, and generate visualizations.

Implemented note types

The OMOP repository has both the raw note text, as well as data structures for NLP artifacts. Implemented note types include: 

• Progress notes  
• Discharge Summaries  
• ED notes  
• H&P  
• Op Note  
• Procedures  
• EEG Reports  
• Solid tumor pathology reports  
• Hematopathology reports  
• Radiology reports (X-ray, CT scan, MRI scan readings)  

Use cases and accessing data

The OHSU data in TriNetX is de-identified. Data from all OHSU clinical sites is included in TriNetX; genetic opt-out patients and affiliate data are excluded. TriNetX users can build queries and obtain patient counts from OHSU and other participating sites prior to Institutional Review Board (IRB) approval. Searchable taxonomies include demographics, diagnoses, procedures and surgeries, medications, laboratory results, patient visits, and vital signs. 

Researchers can use TriNetX to:  

• Assess the feasibility of a study
• Identify patients meeting inclusion/exclusion criteria
• Begin study planning prior to submission to the Institutional Review Board 

After building a cohort, investigators can request row-level patient data or an identified OHSU patient list from the OCTRI RDS team with proper IRB approval. To learn more or to request a dataset, contact octri@ohsu.edu.

TriNetX Training Program

TriNetX Training Program – This robust, comprehensive training program offers additional live and pre-recorded training videos, answers to FAQs, and guidance on common topics. (Note: Requires OHSU TriNetX training and account to access.) 

TriNetX Research Planner

TriNetX Research Planner – This interactive chatbot, designed by researchers at University of California Riverside, is designed to help medical students and faculty plan their TriNetX research projects. 

TriNetX Data Dictionaries

TriNetX Data Dictionaries – This page contains downloadable data dictionaries for each of TriNetX’s main subject areas (demographics, medications, procedures, etc.). (Note: Requires OHSU TriNetX training and account to access.)