The Stanford Medicine data science ecosystem for clinical and translational research

Abstract

Objective: To describe the infrastructure, tools, and services developed at Stanford Medicine to maintain its data science ecosystem and research patient data repository for clinical and translational research.

Materials and methods: The data science ecosystem, dubbed the Stanford Data Science Resources (SDSR), includes infrastructure and tools to create, search, retrieve, and analyze patient data, as well as services for data deidentification, linkage, and processing to extract high-value information from healthcare IT systems. Data are made available via self-service and concierge access, on HIPAA compliant secure computing infrastructure supported by in-depth user training.

Results: The Stanford Medicine Research Data Repository (STARR) functions as the SDSR data integration point, and includes electronic medical records, clinical images, text, bedside monitoring data and HL7 messages. SDSR tools include tools for electronic phenotyping, cohort building, and a search engine for patient timelines. The SDSR supports patient data collection, reproducible research, and teaching using healthcare data, and facilitates industry collaborations and large-scale observational studies.

Discussion: Research patient data repositories and their underlying data science infrastructure are essential to realizing a learning health system and advancing the mission of academic medical centers. Challenges to maintaining the SDSR include ensuring sufficient financial support while providing researchers and clinicians with maximal access to data and digital infrastructure, balancing tool development with user training, and supporting the diverse needs of users.

Conclusion: Our experience maintaining the SDSR offers a case study for academic medical centers developing data science and research informatics infrastructure.

Keywords: data science; electronic medical records; informatics; patient data repositories; team science.

Figure 1.

Overview of the SDSR ecosystem. From left to right: the sources of data that comprise patient timelines, which are processed to create the STARR datasets that can be retrieved and analyzed using community and internally developed tools. These processing systems, datasets and tools are maintained on a secure computing infrastructure. Consulting support in the form of informatics and analytics services, user training, and office hours, is provided.