2013 IT Innovation Contest

A team-based contest for creative IT solutions

CoPathFinder: Enabling innovative translational research via the creation of a searchable pathology database.

Proposal Status: 

Description: Hypothesis-driven science in translational/clinical research is heavily dependent on large searchable electronic databases of clinical information.  UCSF is among the pre-eminent centers for both basic and translational research in the health sciences in part because of its foresight in implementing and maintaining such databases.   Notably, the CoPath database maintained by the department of pathology is critical to many multidisciplinary -and multi-center- translational research efforts involving the departments of pathology, surgery, radiology, transplant medicine, neurology, hematology/oncology, and many others.  At this time, however, no API exists for end-users such as faculty, staff, or residents involved in research projects to search the CoPath database themselves: rather, all searches must be performed by an IT staff member and yields only the most rudimentary information (ie, surgical case numbers only).  This approach is needlessly tedious for both IT and clinical investigators and impedes all research efforts involving the department of anatomic pathology.  We therefore propose the creation of an API accessible to suitably trained end-users for searching the CoPath database in order to harness the tremendous potential of such an interface to spur innovative clinical research.



1. Database of CoPath data separately housed from the native CoPath database by the department of anatomic pathology.

2. User-friendly API for use by clinical investigators to search the database    .

3. Secure data storage of all search data.

4. Mechanism for tracking performed searches by pathology IT.

5. Secure user login requiring registration and training by pathology IT.

6. Training materials (in the form of a pdf document and an audio-visual powerpoint slide show   accessible online) to reiterate patient safety and HIPAA compliance.


Impact on UCSF’s mission and/or community:

UCSF’s mission: UCSF advances health worldwide through innovative health sciences education, discovery and patient care.

1. Completion of this project will promote innovative translational/clinical discovery by unlocking clinical data for investigators and encouraging early hypothesis-driven inquiries to spur new research directions.

2. By enabling investigative inquiry among properly trained UCSF residents and medical students, this project will also promote self-directed education/training in translational/clinical research.

3. The collaborative nature of nearly all modern translational/clinical research studies means that the impact of this project extends to all collaborators of the UCSF department of anatomic pathology, including nearly all UCSF medical center/research departments, pathology and other departments at dozens of partner universities, and industry collaborators.

4. CoPath databases are in use at hospitals throughout the U.S. and the world: distribution of this API to other CoPath users will thus promote innovative research worldwide.


Team Members:

- Ben Buelow, MD, PhD


    -Subject matter expert (pathology resident, clinical investigator)


- Dianna Ng, MD:

    -Subject matter expert (pathology resident, clinical investigator)


- Gavin Law:


- Sebastian Geiger (non-UCSF):



Advisory Panel:

Enrique Terrazas, Residency director, Department of Lab Medicine

Angela See, Director of Clinical Operations, Department of Pathology

Vicky Kirby-Martin, Privacy Office

Tim Hoffman, IT, Medical Center Security

Sunny Bang, IT, Database management

Taylor Sittler: Programming consultant


I think this project would benefit a very broad spectrum of those UCSF faculty outside of the pathology department.  This would also add considerably to our long-standing efforts in "tissue-banking" within the Cancer Center, as it would now provide a much easier way to access potential tissues from the archives.   

Consider scoping the existing database for the potential to add views directly into the operational data to keep data in one location and authoritative, backed-up, and accessible.


Creating a duplicate of the authoritative data by separating out a "Database of CoPath data separately housed from the native CoPath database by the department of anatomic pathology" has the potential for adverse indications such as:

   1. Requiring updates at pre-determined times (which could be a bulk copy but cause a strain to operational database) to refresh the data and keep it consistent and relevant.

   2. Potentially causes confusion for the IT staff regarding which Database is to be supported in the event of trouble.

   3. While Views are typically lightweight - the creation of a copy of the data is likely to be more than a simple bulk copy operation - and could lead to issues with the existing operational database.

As a separate note: consider making the training an audio visual presentation, of short duration, to cover the specifics - such that it is readily available to the community and easy to consume.


Best Regards,





As before, great, helpful comments.  The issues you bring up were discussed extensively with the programmers on our team and Angela See (Chief of Clinical Operations for pathology); the general consensus from day 1 by pathology IT has been that making a copy of the database, with regular/periodic updates, is preferable to interrogating the native database because of concerns regarding detrimental effects of searches on the day to day clinical use of the native database.  Since our priority is -and will always remain- fulfilling our clinical responsibilities to the best of our abilities, we cannot afford to generate this kind of interference for research purposes.

That being said, given your experience with these sorts of issues I will revisit the issue with Gavin and Sebastian and see how they weight the costs/benefits of each approach.

Regarding your comment on training materials: I completely agree that an A-V presentation, accessible on the Department website, will be the ideal training medium.



Ben Buelow

Selected comments from Reviewers:

More relevant to researchers, too narrow focus/benefit

Commenting is closed.