2020-2021 Research Data Series

The “2020-2021 Research Data Series” via Zoom, serves the purpose of disseminating important information about UCSF’s rich offerings for research data resources.  Slides and videos are available for online on-demand viewing and reference for past events. 


2021 Session List:

May 17, 12 - 1 PM   |  New COVID Data for Research 

Several data sources are available for COVID-19 research. In this session, we will review the data sources -- including UCSF, San Francisco DPH, California Department of Health (CDPH) and national COVID data. We will describe the sources of this data, where they are stored, how to gain access and researchers will show exemplar use cases. This session builds on prior COVID webinars and more information will be published here. 

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Feb 24, 1-2 PM  |  EMERSE and Exploring UCSF Clinical Notes

We now have a large set of clinical notes from the UCSF Electronic Health Record (EHR), APeX, that have had identifiable data redacted via an algorithm developed by our data scientists at the Bakar Institute. You can now use this set of 65 million notes for research projects, with IRB approval. If you are a programmer, direct access via MongoDB is available. Another non-technical tool called EMERSE (Electronic Medical Records Search Engine), is available to query the text, with no programming skills required. In this webinar, we will describe the data, how to apply for access, and provide a quick demo of how EMERSE works.

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2020 Session List:

August 19, 1-2 PM  |  COVID-19 Data Sources at UCSF 

UCSF has several data sources available for COVID-19 research. In this session, we will review the data sources -- including UCSF COVID-19 Data Mart, UC-wide CORDS data, and de-identified data for research. We will describe the sources of this data, the structures where they are stored, and how to gain access. We will do a deep dive into working with UCSF COVID-19 Data Mart, and show a git repository with sample code, which can give you a fast start to analyze the data. Login to see SLIDES AND VIDEO 

August 21, 2-3 PM  |  De-identified Clinical Data Warehouse and OMOP 

This session will feature an overview of the structured de-identified UCSF research data assets, De-Identified Clinical Data Warehouse, and De-Identified OMOP. We will go over data pipelines, general scope, structure, and limitations of each data asset, as well as support resources available for the UCSF research community. We will then illustrate the use of the DEID CDW and OMOP data with a few research use cases. Login to see slides and video

September 10,  3-4 PM  |  Mapping COVID-19: UCSF Health Atlas and Citizen Science Study  

In this session, learn about how mapping COVID-19 data in the context of population health factors can help elucidate the drivers of the pandemic. Login to see slides and video

September 14, 2:30-3:30 PM  |  UCSF Research Data Overview

Our annual overview of the resources, including data, tools, compute, and support available to you at UCSF and how to get started. login to see slides and video

September 16, 2-3 PM  | UCSF High Performance Computing Environments

Overview of options including Wynton, AWS, and RAE (the new MyResearch) Login to see slides and video

September 21, 10-10:45 AM  |  Meet RAE - The New MyResearch  

The MyResearch platform you already know and love has just gotten better - meet RAE. Short for Research Analysis Environment, RAE offers free, premium, and new AWS cloud options to support UCSF researchers and collaborators. Join us for a demo and discussion of how RAE’s secure data hosting and compute services can support your research needs. Login to see slides and video

September 30,  3-4 PM |  Information Commons and AI Modeling  

Information Commons is a fast and easily searchable and accessible repository of all UCSF clinical data and models, and related basic science and population data, that enables UCSF research and discovery of new health insights underlying precision medicine, to improve patient and health care. Login to see slides and video

Join this session to learn about "data sharing," from 1) sharing research data with external partners, 2) taking in research data from somewhere else, and 3) requirements for sharing data for reproducibility of results, as required for publication. Experts from Privacy, IRB, Academic Research Systems, Security, Contracts, & Library will answer your questions!  Login to see slides and video

October 20,  2:30 - 3:30 PM |  Medicare Data and other External Data Sets

Join us for an overview of various pathways (and their tradeoffs) to accessing CMS and MarketScan Data at UCSF.  Joanne Spetz PhD will share information about the datasets and on how to access them for your own research.  Login to see slides and video

Learn about PatientExploreR, an application that produces patient-level interactive and dynamic reports and visualization of clinical data, without requiring programming skills.  Login to see slides and video

October 29,  1:30 - 2:30 PM |  Navigating Digital Innovation at UCSF: One researcher's experience

Hear one frontline innovator describe her efforts to develop, deploy and study digital innovations in the clinical environment here at UCSF. Learn more about the budgeting, timelines, buy-in and approvals necessary.  Login to see slides and video

October 30,  2 - 3 PM |  Images and Tools in the Imaging Commons

Learn about how to access UCSF's shared repository of clinical images and the tools available for image analysis. Login to see slides and video 

November 3,  11 - 12 AM |  Building SMART on FHIR Apps at UCSF

Interested in leveraging FHIR to build and integrate digital health apps at UCSF? Come hear two developers walk through their process in creating a new SMART on FHIR app. Login to see slides and video 

November 4,  1 - 2 PM |  UCSF GitHub available now!

Learn about UCSF on-premise GitHub, which is safe for patient data and proprietary code.   Login to see slides and video

 Check back here for upcoming sessions on:

  • population health data
  • molecular and 'omics data
  • access to clinicial notes