Remarkable progress that cements our growing reputation as the leading biomedical research data platform world-wide.
Information Commons Wynton
After a successful pilot, we are happy to introduce our new on-premise, interactive data science environment, the Information Commons Wynton. This Wynton-based, scalable application server features access to UCSF de-identified clinical data, including medical imaging, clinical notes, structured EHR data, biomedical reference data, and more. Learn more, request access, and join the user tutorial on January 19.
This platform, governed by the Research Data Science Council, is the result of work by a dynamic team (below) from BCHSI, CTSI, UCSF IT, UCSF Library, Radiology, SOM Tech and Wynton Ops
Imaging Commons
The new Imaging Commons is now live.
The first cohort of de-identified clinical images — brain MRIs of patients diagnosed with a type of brain tumor known as CNS lymphoma — is now in the Information Commons, thanks to the joint effort of the Imaging Commons – a collaboration between the Center for Intelligent Imaging (CI2); BCHSI; Reza Eghbali, PhD, from the Innovate for Health Data Science Health Innovation Fellowship; and Andreas Rauschecker, MD, PhD, of the Department of Radiology and Biomedical Imaging. This database of images, linked directly with de-identified clinical laboratory and demographic information pre-existing in Information Commons, will allow researchers to build models for prognostication of this life-threatening disease, with the ultimate hope of guiding clinicians in treatment.
This initiative is led and supported by the Radiology Department leadership: Sharmila Majumdar, PhD, and Christopher Hess, MD, PhD; and the UCSF Center for Intelligent Imaging under the technical leadership of Jason Crane, PhD; James Hawkins; and Beck Olson.
The pipeline will process images continuously, onboarding new cohorts based on requests from UCSF researchers. We welcome you to request an imaging cohort for de-identification and addition to the Information Commons.
Clinical Notes
UCSF de-identified clinical notes will be available to our research community by the end of January, 2022. The 110+ million UCSF clinical notes are being re-processed with the newly certified de-identification algorithm.
The notes will be accessible from the Information Commons and user workstations via the user-friendly EMERSE, and programmatically via the Solr API.
This work completes an enormous effort pioneered by Atul Butte, MD, PhD, and his then-PhD-student Beau Norgeot, PhD, which is detailed in this publication.
Our purpose is to support your research. We are grateful for the opportunity to collaborate with such inspiring researchers, engineers, and data scientists. BCHSI also recognizes and appreciates the close partners of the BCHSI Information Commons team, above, who enabled and implemented this year’s initiatives. We look forward to the results that lie ahead in 2022, thanks to this IC Data Science Platform and all who support this unique resource.
The BCHSI Information Commons is grateful to the following individuals and their respective teams, among the many others who support our work.
| Albert Lee
Alina Goncharova Andreas Rauschecker Angela Rizk-Jackson Atul Butte Beau Norgeot Beck Olson Beth Berrean Bill Santo Boris Oskotsky Brian Chan Brian Turner
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Christopher Hess
Dana Ludwig Dima Lituiev Edna Rodas Ellen Clary Eric Meeks Eugenia Rutenberg Evan Phelps Geoff Boushey Gundolf Schenk Hunter Mills James Hawkins |
Jason Crane
Jennifer Creasman Karla Lindquist Kasturi Balakrishnan Kim Romero Lakshmi Radhakrishnan Leslie Yuan Nelson Lee Nicki Martin Oksana Gologorskaya Pablo Damasceno Remi Frazier |
Reza Eghbali
Rhett Hillary Rick Larsen Saketh Koduru Sandeep Giri Scooter Morris Sharat Israni Sharmila Majumdar Yelena Zayakina Yongmei Shi
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