The ACTRI provides a wide range of data services to support research. We can help you at all stages of your study, from cohort identification to data collection to results analysis and storage.
This Health Data Portal will introduce you to our services and help you get started.
COVID-19 research data available to the UCSD research community. Read more
Work with your research data in a secure, HIPAA-compliant virtual environment. Read more
ACTRI and HS Information Services partnered with the Department of Radiology to add radiology images (CT, MRI, plain radiographs) to the DECS service
Patient data extracts for research analysis. Read more
Build and manage online surveys and forms. Read more
Integrated software for managing clinical research trials and studies. Read more
Identify eligible patients for clinical trials from a nationwide network. Read more
Data visualization tool – turn dry data into vibrant charts and diagrams! Read more
UC Health Data Warehouse (UCHDW)
The UCHDW currently holds data on nearly 6 million patients seen at a UC facility since 2012. These patients received care from nearly 100,000 health care providers in over 200 million encounters, with nearly 200 million procedures, more than half a billion medication orders, and with over 2 billion vital signs measurements and test results. Over 600,000 of these patients are primary care patients.
Access to this information requires technical familiarity and ability to write code in R, Python, or Spark SQL, that queries the deidentified clinical data. The BMI team may assist to provision access directly to the UCHDW data. If assistance is needed in preparing the customized queries, there will be a recharge fee.
To request access, please submit Biomedical Informatics->UCHDW request form
Aggregated Registry for Molecular Oncology Research (ARMOR)
ARMOR is a large-scale data registry designed to advance precision oncology. ARMOR aggregates clinicopathological and clinical genomics data from the Electronic Health Record using automated and real-time collection of both molecular and clinical information. This resource enables UCSD Health investigators to rapidly validate research findings in an independent, real world patient population, develop predictive models, test novel therapeutic paradigms and document patient trajectories.
ARMOR is available to UCSD investigators through a UCSD cBioportal instance hosting de-identified clinical genetic results and partial clinical information from patients who underwent tumor sequencing as part of their clinic care. Source data can be accessed by approved users through the ACTRI Virtual Research Desktop. ARMOR is approved under the Molecular Oncology Registry protocol (UCSD IRB 200373) and maintained by the Center for Computational Biology & Bioinformatics with support from the Moores Cancer Center, Altman Clinical & Translational Research Institute and Vice Chancellor for Health Sciences.
Request Access - submit request form
Kathleen Fisch, Ph.D., Faculty Director, Center for Computational Biology & Bioinformatics (email@example.com)
Adam Mark, M.S. Senior Bioinformatics Engineer, Center for Computational Biology & Bioinformatics (firstname.lastname@example.org)
The ARMOR registry has been presented at the 2022 American Medical Informatics Association annual meeting, as a poster.
Phillips S., Xu X., Kenkre R., Paul P., Zhu W., Hogarth M., Harismendy O. Integrating Molecular and Clinical Data for Real World Evidence Research In Precision Oncology (2021), Poster presented at the 2021 annual meeting of the American Medical Informatics Association.
De-identification: The genetic data is directly extracted from the content of the clinical report received from the testing laboratory and should match the clinical data with high accuracy. The clinical and demographic data are extracted from the electronic health records and de-identified following the NIH Safe Harbor method. In particular, the date of the first molecular report is used as the anchor date for each patient. All other dates are expressed in days since anchor date. The ARMOR user is invited to read the release notes below in order to understand some of the limitations and possible inaccuracies that may result from this process. The use of the ARMOR registry is for research only and users should not attempt to re-identify patients or share the results with other investigators.
Aggregation: Reports from different types of tests are aggregated. It is the user's responsibility to identify genes and mutations covered and not-covered by each test and consider the possibility of False Negative findings in the results.
Prescriptions: antineoplastics and endocrine specific prescriptions were abstracted to their active ingredients. Prescription start dates were de-identified as days from the anchor date. In absence of a reliable end date, the duration of the treatment was automatically inferred, by extending sequential prescriptions, provided the time interval is shorter than a drug holiday threshold. The drug holiday threshold was inferred from drug-specific outlier time intervals across all patients.