The ACTRI Health Informatics (HI) program is revolutionizing clinical research data management by seamlessly integrating research workflows into the electronic health record (EHR). This approach bridges the gap between clinical practice and research, enhancing safety, efficiency, and collaboration. 

In 2021, ACTRI led UCSD’s transition from a stand-alone Clinical Trial Management System to Epic’s full Research Module, becoming one of the first academic institutions to launch this advanced system. This integration, fully implemented at UCSD’s Moores Cancer Center, enables clinicians treating ACTRI research participants outside clinical trial activities to access essential research information. 

A key regional asset in this effort is San Diego Health Connect, a Health Information Organization that facilitates health data exchange among regional EHRs, including those of partner hospitals (ECRMC, Eisenhower Health, and RCH). This exchange enhances safety by providing admission notifications, alerting clinicians to drug interactions, and informing them of patients' trial participation. It also supports research on populations with fragmented care (e.g., individuals experiencing substance use, homelessness, or undocumented status) and helps identify community priorities. 

To guide these efforts, we conduct strategic planning retreats and surveys with investigators, ensuring that our initiatives address the most pressing needs and priorities in health informatics. 

The ACTRI Health Informatics (HI) program is creating a robust informatics environment to collect real-world data (RWD) and drive meaningful insights for clinical research. 

Our innovations include: 

• Real-Time Bedside Data Monitoring: As a national leader in this field, we enable prompt analysis of streaming data from bedside devices using an interface engine that converts device signals into Health Level 7 messages, stored in a secure database. 

• Secure Virtual Research Cloud: In 2018, ACTRI led UCSD to become one of the first institutions in the U.S. to implement an "air-gapped" private virtual cloud for research involving sensitive healthcare data. The UCSD Health Secure Research platform allows investigators to securely analyze protected health information using tools like R, SPSS, and Python, with access restricted to multi-factor authenticated virtual desktops. 

• Nightingale Program: Developed in collaboration with the UCSD IRB and Research Compliance, this program provides investigators access to secure, de-identified EHR datasets. These datasets, harmonized to the OMOP v5.4 structure, can be analyzed using SQL, R, and Python via the Nightingale platform or virtual research desktops. 

• Access to UC-Wide Data: Through our collaboration with UC BRAID, ACTRI investigators can analyze de-identified data from over 9 million patients across the UC system using a secure research enclave. 
  • To request access, please sign up here and send questions to the Application Support Team.

Building Expertise Through the Nightingale Intern Program 
Recognizing the programming expertise needed for complex data analysis, we partnered with the UCSD School of Engineering to establish the Nightingale Intern Program. This initiative trains and employs undergraduate students to support investigators in data analysis. Supervised by Dr. Mike Hogarth, these interns are highly skilled in programming and quickly adapt to the Nightingale data models, enabling research teams to maximize the utility of available datasets. 

By fostering secure and innovative data access, the ACTRI is advancing real-world data analysis, accelerating discovery, and empowering clinical researchers. 

We are advancing participant engagement and research activities by developing innovative mobile platforms that streamline communication and data collection. 

Our approach includes: 

• Participant-Researcher Communication Tools: A suite of mobile platforms facilitates real-time communication between researchers and study participants, improving engagement and simplifying the collection of clinical data. These tools integrate participant data seamlessly into the Clinical Trial Management System and electronic health records (EHR). 
  • • OpenClinica - EDC/Epic  direct connections  over HL7
    • Patient Reported Outcome (PRO) Module

• TrialFinder: Customized by the ACTRI from UC BRAID’s original tool, TrialFinder allows patients to identify clinical trials and contact research teams directly. This tool receives over 200 patient queries each month about clinical trials at ACTRI. 

• Simplified Study Enrollment: ACTRI supports electronic consent platforms like DocuSign and REDCap, which include features such as video explanations and online consent forms. These tools simplify the enrollment process for participants and ensure research procedures are clearly explained. 
  • Docusign
  • REDCap

By leveraging mobile technology, we are addressing challenges to participation, improving clinician engagement, and making clinical research more accessible to all. 

To address the growing volume and complexity of research data, we are developing a next-generation, integrated clinical data repository that ensures data quality, robust cybersecurity, and formal data provenance through:

• High-Performance and Secure Computing: We leverage a combination of on-premises HIPAA-compliant cloud resources, cloud computing services like AWS, and distributed frameworks such as ENACT and TriNetX to manage and process large-scale data. 

• Ensuring Data Quality: Advanced quality control mechanisms—such as data validation rules, outlier detection algorithms, and missingness reconciliation—guarantee the accuracy, consistency, and completeness of data, improving the validity and reliability of research findings. Many of these methods are generalizable and are being implemented across the Clnical and Translational Science Award network through ENACT. 

• FAIR-Inspired Data Access: We provide standardized datasets aligned with Findability, Accessibility, Interoperability, and Reuse (FAIR) principles. To support investigators in utilizing these datasets, our Nightingale Interns—undergraduate computer science and engineering students—are trained to assist with querying and processing data using SQL, R, and Python. The integration of Jupyter notebooks with Nightingale datasets enables advanced visualization of data, enhancing usability and insights. 

• Enhancing Rigor and Reproducibility: To address challenges in the field, we implement standardized data acquisition protocols, rigorous curation techniques, and best practices for health informatics methods. These efforts improve the reproducibility of research findings, reduce biases, and enable comparison and integration of results across studies. 

By combining cutting-edge technology, data security, and robust training programs, we are creating an advanced informatics environment that fosters reliable and impactful clinical research. 

We are transforming the way researchers interact with multimodal research data repositories by developing a next-generation data analysis platform equipped with advanced tools, including Large Language Model (LLM)-assisted “conversational” querying. 

Our approach includes: 

• Secure Access to Real-World Data (RWD): The Nightingale enclave provides rapid, self-service access to de-identified datasets from over 1.2 million UCSD EHR records, compliant with IRB and HIPAA waiver regulations. These datasets are harmonized and made available within a secure, user-friendly environment. 

• Conversational Querying: To simplify data analysis, we are developing LLM-assisted tools that allow investigators to query data using natural language instead of programming languages like SQL or R. This innovation reduces barriers for researchers, enabling faster and more intuitive data exploration. 

• Natural Language Processing (NLP) Capabilities: De-identified clinical notes from the dataset can be analyzed using advanced NLP systems, including: 

• Apache Clinical Text Analysis and Knowledge Extraction System (cTAKES) 

• Clinical Language Annotation Modeling and Processing (CLAMP) 

• AWS Comprehend Medical 

Researchers also have access to expert consultation to integrate NLP methods into their studies, enhancing the scope and depth of their analyses. 

By empowering researchers with these cutting-edge tools, we are fostering new discoveries and insights from complex datasets, ultimately accelerating the pace of clinical research. 

To ensure semantic interoperability and improve the utility of research data, the ACTRI prioritizes the use of shared ontologies and Common Data Elements (CDE). 

Our approach includes: 

• Pioneering Standardization Initiatives: The ACTRI played a leading role in the UC-Research eXchange (ReX) project, which was among the first efforts to use standardized ontologies to harmonize real-world data (RWD) across multiple data warehouses within the UC BRAID. This foundational work later evolved into the Accrual to Clinical Trials (ACT) CTSA consortium project, and subsequently into the ENACT program. 

• Leadership in National Projects: As a co-leader in the ENACT initiative, the ACTRI oversees regulatory issues and the development of nationwide ephemeral data enclaves, leveraging shared ontologies to standardize data annotations and ensure semantic alignment across institutions. 

• Refining Data Governance: These experiences have informed our robust data governance processes, ensuring that institutional clinical and research data adhere to high standards of semantic interoperability. 

By advancing shared ontologies and CDEs, the ACTRI addresses key challenges in Clinical and Translational Science (CTS), paving the way for innovative solutions and more impactful research collaborations.