Powering Innovation and Translational Science with OCTRI Informatics

A data dashboard visualized above a laptop with a hand on the laptop.

Mission and goals

OCTRI Informatics accelerates translational research by providing a full suite of informatics tools for bench-to-bedside, clinical, and health care systems research. The program achieves its objectives by:

Helping researchers leverage EHR/Epic data for studies.
Developing software and customized databases for clinical research data collection and management.
Assisting researchers with the storage, retrieval, sharing, and optimal use of biomedical information, data, and knowledge.

We encourage you to meet with program staff early in the study planning stage to ensure an appropriate solution design and budget. Please submit a request for an informatics consultation. 

For more information on this program's mission and goals, please review the OCTRI Informatics Strategy document.

Innovation Core: Custom applications and research repositories to meet complex needs

The OCTRI Informatics Innovation Core supports a diverse population of investigators and projects using an array of innovative technologies. We have the staff and expertise to create and maintain sophisticated software applications and databases. Review our services below.

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.

Hosting data in a research repository can serve as a source of truth for published results and provide insights into the study population through reports and exploration.

Access controls can be used to ensure that only your team can log in, with roles and permissions controlling what each member can see and do.

Repositories can be populated with data from the EHR and regularly updated as new encounters occur in Epic.

The Innovation Core can create a custom application to ease the burden on study staff managing clinical research data.

A web interface allows for quick browsing and entry of data, and custom imports can be created to bring spreadsheets into a structured and auditable format with security and regular backups built in.

These systems can also integrate with other resources like the Research Data Warehouse to pull in demographics, labs, and genomics data automatically or data pipelines in R or Python to perform analysis or build reports.

Visualizing your data often reveals important insights that may not be immediately obvious. We will work with you to structure and visualize your data.

Read more about data dashboards here or see project spotlight below on a project with an OHSU faculty member.

If your study requires an application to support either the data collection or exploration of a domain, we can deliver a custom solution that meets OHSU regulatory and security guidelines.

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 have expertise in navigating OHSU regulatory and security requirements. We can also provide an estimate to support your grant application, including longer term collaborations funded by FTE on a grant.

User roles and permissions
Integrations with other systems, including FHIR applications
User controlled managed content
Reporting functionality

HIPAA compliance and IRB expiration monitoring

Hosting/Maintenance
Secure coding practices

Authentication/Security*
Auditing*

(*) required by OHSU

To reach the Innovation Core, please contact an OCTRI Navigator

503-418-9790
octri@ohsu.edu

Resource Request Form

Innovation Core Project Spotlight

Customized COVID-19 Vaccine Serology Dashboard

COVID-19 data dashboard with a COVID-19 virus behindbar, circle, and line graphs.

The OCTRI Informatics Innovation Core collaborated with OHSU infectious disease expert, Dr. Marcel Curlin, to build a database from thousands of blood samples collected from employees before and after COVID-19 vaccination.

The resulting COVID-19 Vaccine Serology Dashboard provides both study participants and the study team a centralized place for accessing and tracking data.

Review the full story and dashboard examples in the Project Spotlight Summary

Research Data Warehouse: Using Epic® data for research purposes

OCTRI maintains a repository of Epic data from patients and research subjects. This valuable resource, called the Research Data Warehouse (RDW), provides access to over 2.5 million patient records with 20 million patient encounter records and more than 40,000 data points. OCTRI staff can act as your guide through this complex data, or you can query the data yourself with the Cohort Discovery Tool.

You can use the RDW for a broad range of research purposes, including:

Cohort discovery (counters) for preparation to research purposes
Deidentified data sets for epidemiological studies
Data sets that identify potential study participants or gather retrospective data on current participants
Automated data marts and/or data feeds that provide up-to-date population demographics for individual research projects
Natural language processing applications for electronic health record notes

Data Type	RDW Count	OMOP Count*
Total patients	4M	3.9M
Inpatient encounters	285K	406K
Emergency encounters	627K	614K
Outpatient encounters	107M	80.5M
Lab results	340M	209M
Microbiology	3.5M	NA
Medication results	69M	76M
Total diagnoses	206M	84M
Total procedures	243M	127M

*More on OMOP below

To reach the RDW team, please complete the OCTRI Resource Request Form or email: octrihlp@ohsu.edu

Cohort Discovery Tool

Cohort Discovery is a web-based tool that allows OHSU researchers to discover patient cohort counts from RDW-based Epic data for preparatory to research purposes. 

Cohort Discovery Login

Researchers can use this tool to:

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

The data is deidentified, but patient data sets can be extracted from saved searches with proper Institutional Review Board approval.

Searchable taxonomies include demographics, diagnoses, medications, procedures, laboratory results, surgeries, patient visits, and vital signs.

Cohort Discovery users must take part in a brief training prior to gaining access. Virtual tutorials are offered once a month via WebEx.

Use Compass to register by searching "Cohort Discovery". Registration for training closes three days prior to training date.

Upcoming training sessions

12/04/2024

OCTRI Cohort Discovery Training

1/16/2025

OCTRI Cohort Discovery Training

2/11/2025

OCTRI Cohort Discovery Training

Natural Language Processing applications

The RDW leverages an OMOP data repository to access extensive electronic health record notes for usage in Natural Language Processing (NLP) applications.

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)

The Observational Medical Outcomes Partnership (OMOP) Common Data Model (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). We have implemented the OMOP CDM at OHSU and provide access to its de-identified data for research uses. We are in the process of implementing software tools to allow access to the data, perform analysis, and generate visualizations.

Recent enhancements have included augmenting the data with social determinants of health data, demographic data (REALD), and other valuable data sets.

Partner with OCTRI on clinical research data initiatives

OCTRI Informatics and the OHSU Knight Cancer Institute have formal collaborations around clinical research data enhancement and natural language processing that leverage the RDW, as well as expertise and strengths within each institute. Read more about the OCTRI-Knight partnership below.

If you are interested in developing a partnership similar to the one with the Knight Cancer Institute for your center, department, or division, then please contact Dr. Mohammad Adibuzzaman, co-Director of OCTRI Informatics: adibuzza@ohsu.edu

Knight Data Enhancement Pilot 2019

OCTRI Informatics and the OHSU Knight Cancer Institute launched a Knight Data Enhancement Pilot in July of 2019. The premise for this pilot was to:

Ensure data from the RDW were available to IRB approved protocols in a timely and accurate fashion
Provide dedicated analyst support to assist in discovery of additional data elements needed for Knight clinical and translational research
Improve efficiency for data curators by use of data feeds and support from natural language processing (NLP)
Maximize the use of the OHSU Research Data Warehouse to support the mission of the Knight Cancer Institute

The initial focus was to automate manual data pulls from the RDW into the Knight Data Management system (Knight DMS). The use case for the pilot was the Serial Measurements of Molecular and Architectural Responses to Therapy (SMMART), the flagship project of the Knight Cancer Institute’s precision oncology program. This was done by the Knight funding 2 FTE in the OHSU Research Data Warehouse Team to provide data engineering and analyst support for Knight Data Operations. The pilot proved to be cost effective, allowed scaling and reduced errors. This automated 9 previously manual data feeds, as well as creating 3 new automated data pulls, given the dedicated analyst support.

Knight Data Enhancement Program 2020

Based on this early success, the Knight Data Enhancement Program (DEP) was formed in January 2020 as part of the Knight Strategic planning computational roadmap, co-lead by Dr. Shannon McWeeney, Chief Data Officer for the Knight. This program actively supports SMMART, Brenden-Colson Center for Pancreatic Care , BeatAML, and other key Knight Cancer Institute programs and efforts. It was critical for the Cancer Covid-19 Consortium during the height of the pandemic. Overall, the DEP and its integration with Knight DMS has led to a 5X increase in efficiency for incorporating new data elements/feeds. In addition, the Knight leverages its partnership with OCTRI NLP for unstructured data.

For Knight investigators wishing to learn more about Knight DEP, please contact Dr. Christina Zheng, Director of Knight Data Operations: zheng@ohsu.edu.

RDW Project Spotlights

Opioid treatment

Customized database of patients with opioid use disorder to identify potential treatments

Cartoon of two physicians standing on either side of a large pill bottle with pills on the ground, a cloud coming out of the bottle, and a data network floating above the cloud.

The OCTRI RDW team collaborated with Dr. Ryan Cook, OHSU additiction medicine expert, to build a database of 10,000+ patients with opioid use disorder containing information on medical services, lab tests, medications, hospital stays, clinical notes, social determinants of health, and more.

This database will be used to identify which interventions may most effectively reduce drug use and promote engagement in substance use disorder care.

Read the full story in the Project Spotlight Summary.

Maternal health

Customized dataset for study of postpartum maternal health

The OCTRI RDW team helped DMICE faculty, Dr. Nicole Weiskopf, and her trainee, Ayo Babatunde, an OHSU researcher assess data requirements necessary to answer research questions related to maternal health during the postpartum period and supported the data extraction process.

This data set will be used for a retrospective study to identify and understand threats to validity when studying maternal morbidity.

Read the full story in the Project Spotlight Summary.

TRANS Registry

Customized registry of patients seeking gender-affirming surgery to study patient outcomes

The OCTRI RDW team collaborated with Dr. Geolani Dy, OHSU Associate Professor of Urology, to build a multi-site, prospective, observational registry of individuals seeking gender-affirming vaginoplasty and vulvoplasty.

This database will be used to answer questions about gender-affirming surgery outcomes that are meaningful to patients, clinicians, and healthcare systems.

Read the full story in the Project Spotlight Summary.