Biospecimen Annotation Standard for Medical Research

April 12, 2016

Under the leadership of Dr. Katherine Nathanson and Dr. Michael Feldman, a Perelman School of Medicine biospecimen annotation standard was developed and released in March 2016. The goal of the standard is to promote consistency across the institution in terms of specimen annotation and sharing of biospecimen data across medical research projects at Penn and with other institutions.

The standard was developed in a series of workshops attended by several in-house biospecimen lab managers, bio-informaticians, Dr. Christian Stoeckert (Genetics, IBI), and Drs. Nathanson and Feldman. It borrows heavily from the NCI CATissue package, the NCI CDEBrowser data, and established data annotations used by pre-existing repositories at Penn. All permissible values (for example, body site locations) are also mapped to ontologies to allow for flexible data analytics.

For more information on the PSOM Biospecimen Annotation Standard visit the Tumor Tissue/ Biospecimen Bank webpage.
For information on acquiring a PSOM sponsored biospecimen database to manage your research samples, contact Jason Hughes, Director, Enterprise Research Applications & High-Performance Computing, or the Penn Medicine Academics Computing Services (PMACS).