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An informatics supported web-based data annotation and query tool to expedite translational research for head and neck malignancies

Waqas Amin1*, Hyunseok P Kang5, Ann Marie Egloff4, Harpreet Singh1, Kerry Trent13, Jennifer Ridge-Hetrick4, Raja R Seethala2, Jennifer Grandis3 and Anil V Parwani12

Author Affiliations

1 Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA

2 Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA

3 Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA

4 Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA

5 Roswell Park Cancer Institute, Buffalo, NY. USA

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BMC Cancer 2009, 9:396  doi:10.1186/1471-2407-9-396

Published: 13 November 2009



The Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets.


The various components of this annotation tool include the Development of Common Data Elements (CDEs) that are derived from College of American Pathologists (CAP) Checklist and North American Association of Central Cancer Registries (NAACR) standards. The Data Entry Tool is a portable and flexible Oracle-based data entry device, which is an easily mastered web-based tool. The Data Query Tool helps investigators and researchers to search de-identified information within the warehouse/resource through a "point and click" interface, thus enabling only the selected data elements to be essentially copied into a data mart using a multi dimensional model from the warehouse's relational structure.

The SPORE Head and Neck Neoplasm Database contains multimodal datasets that are accessible to investigators via an easy to use query tool. The database currently holds 6553 cases and 10607 tumor accessions. Among these, there are 965 metastatic, 4227 primary, 1369 recurrent, and 483 new primary cases. The data disclosure is strictly regulated by user's authorization.


The SPORE Head and Neck Neoplasm Virtual Biorepository is a robust translational biomedical informatics tool that can facilitate basic science, clinical, and translational research. The Data Query Tool acts as a central source providing a mechanism for researchers to efficiently find clinically annotated datasets and biospecimens that are relevant to their research areas. The tool protects patient privacy by revealing only de-identified data in accordance with regulations and approvals of the IRB and scientific review committee.