A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network

Thomas A. Drake, Jonathan Braun, Alberto Marchevsky, Isaac S. Kohane, Christopher Fletcher, Henry Chueh, Bruce Beckwith, David Berkowicz, Frank Kuo, Qing T. Zeng, Ulysses Balis, Ana Holzbach, Andrew McMurry, Connie E. Gee, Clement J. McDonald, Gunther Schadow, Mary Davis, Eyas M. Hattab, Lonnie Blevins, John HookMichael Becich, Rebecca S. Crowley, Sheila E. Taube, Jules Berman

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

This report presents an overview for pathologists of the development and potential applications of a novel Web enabled system allowing indexing and retrieval of pathology specimens across multiple institutions. The system was developed through the National Cancer Institute's Shared Pathology Informatics Network program with the goal of creating a prototype system to find existing pathology specimens derived from routine surgical and autopsy procedures ("paraffin blocks") that may be relevant to cancer research. To reach this goal, a number of challenges needed to be met. A central aspect was the development of an informatics system that supported Web-based searching while retaining local control of data. Additional aspects included the development of an eXtensible Markup Language schema, representation of tissue specimen annotation, methods for deidentifying pathology reports, tools for autocoding critical data from these reports using the Unified Medical Language System, and hierarchies of confidentiality and consent that met or exceeded federal requirements. The prototype system supported Web-based querying of millions of pathology reports from 6 participating institutions across the country in a matter of seconds to minutes and the ability of bona fide researchers to identify and potentially to request specific paraffin blocks from the participating institutions. With the addition of associated clinical and outcome information, this system could vastly expand the pool of annotated tissues available for cancer research as well as other diseases.

Original languageEnglish
Pages (from-to)1212-1225
Number of pages14
JournalHuman Pathology
Volume38
Issue number8
DOIs
StatePublished - Aug 2007

Fingerprint

Surgical Pathology
Informatics
Pathology
Paraffin
Unified Medical Language System
Aptitude
National Cancer Institute (U.S.)
Confidentiality
Research
Information Systems
Autopsy
Neoplasms
Language
Research Personnel

Keywords

  • Database
  • Informatics
  • Internet
  • Pathology
  • Tissue bank

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Drake, T. A., Braun, J., Marchevsky, A., Kohane, I. S., Fletcher, C., Chueh, H., ... Berman, J. (2007). A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network. Human Pathology, 38(8), 1212-1225. https://doi.org/10.1016/j.humpath.2007.01.007

A system for sharing routine surgical pathology specimens across institutions : the Shared Pathology Informatics Network. / Drake, Thomas A.; Braun, Jonathan; Marchevsky, Alberto; Kohane, Isaac S.; Fletcher, Christopher; Chueh, Henry; Beckwith, Bruce; Berkowicz, David; Kuo, Frank; Zeng, Qing T.; Balis, Ulysses; Holzbach, Ana; McMurry, Andrew; Gee, Connie E.; McDonald, Clement J.; Schadow, Gunther; Davis, Mary; Hattab, Eyas M.; Blevins, Lonnie; Hook, John; Becich, Michael; Crowley, Rebecca S.; Taube, Sheila E.; Berman, Jules.

In: Human Pathology, Vol. 38, No. 8, 08.2007, p. 1212-1225.

Research output: Contribution to journalArticle

Drake, TA, Braun, J, Marchevsky, A, Kohane, IS, Fletcher, C, Chueh, H, Beckwith, B, Berkowicz, D, Kuo, F, Zeng, QT, Balis, U, Holzbach, A, McMurry, A, Gee, CE, McDonald, CJ, Schadow, G, Davis, M, Hattab, EM, Blevins, L, Hook, J, Becich, M, Crowley, RS, Taube, SE & Berman, J 2007, 'A system for sharing routine surgical pathology specimens across institutions: the Shared Pathology Informatics Network', Human Pathology, vol. 38, no. 8, pp. 1212-1225. https://doi.org/10.1016/j.humpath.2007.01.007
Drake, Thomas A. ; Braun, Jonathan ; Marchevsky, Alberto ; Kohane, Isaac S. ; Fletcher, Christopher ; Chueh, Henry ; Beckwith, Bruce ; Berkowicz, David ; Kuo, Frank ; Zeng, Qing T. ; Balis, Ulysses ; Holzbach, Ana ; McMurry, Andrew ; Gee, Connie E. ; McDonald, Clement J. ; Schadow, Gunther ; Davis, Mary ; Hattab, Eyas M. ; Blevins, Lonnie ; Hook, John ; Becich, Michael ; Crowley, Rebecca S. ; Taube, Sheila E. ; Berman, Jules. / A system for sharing routine surgical pathology specimens across institutions : the Shared Pathology Informatics Network. In: Human Pathology. 2007 ; Vol. 38, No. 8. pp. 1212-1225.
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