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Open Access Methodology article

The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource

Jules J Berman1*, Milton Datta2, Andre Kajdacsy-Balla3, Jonathan Melamed4, Jan Orenstein5, Kevin Dobbin1, Ashok Patel6, Rajiv Dhir6 and Michael J Becich6

Author Affiliations

1 Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA

2 Department of Pathology, University of Wisconsin, Milwaukee, USA

3 Department of Pathology, University of Illinois Medical Center, Chicago, USA

4 Department of Pathology, New York Medical Center, New York, USA

5 Department of Pathology, George Washington University Medical Center, Washington, D.C., USA

6 Center for Pathology Informatics and Benedum Oncology Informatics Center, University of Pittsburgh Medical Center, Pittsburgh, USA

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BMC Bioinformatics 2004, 5:19  doi:10.1186/1471-2105-5-19

Published: 27 February 2004

Abstract

Background

Tissue Microarrays (TMAs) have emerged as a powerful tool for examining the distribution of marker molecules in hundreds of different tissues displayed on a single slide. TMAs have been used successfully to validate candidate molecules discovered in gene array experiments. Like gene expression studies, TMA experiments are data intensive, requiring substantial information to interpret, replicate or validate. Recently, an open access Tissue Microarray Data Exchange Specification has been released that allows TMA data to be organized in a self-describing XML document annotated with well-defined common data elements. While this specification provides sufficient information for the reproduction of the experiment by outside research groups, its initial description did not contain instructions or examples of actual implementations, and no implementation studies have been published. The purpose of this paper is to demonstrate how the TMA Data Exchange Specification is implemented in a prostate cancer TMA.

Results

The Cooperative Prostate Cancer Tissue Resource (CPCTR) is funded by the National Cancer Institute to provide researchers with samples of prostate cancer annotated with demographic and clinical data. The CPCTR now offers prostate cancer TMAs and has implemented a TMA database conforming to the new open access Tissue Microarray Data Exchange Specification. The bulk of the TMA database consists of clinical and demographic data elements for 299 patient samples. These data elements were extracted from an Excel database using a transformative Perl script. The Perl script and the TMA database are open access documents distributed with this manuscript.

Conclusions

TMA databases conforming to the Tissue Microarray Data Exchange Specification can be merged with other TMA files, expanded through the addition of data elements, or linked to data contained in external biological databases. This article describes an open access implementation of the TMA Data Exchange Specification and provides detailed guidance to researchers who wish to use the Specification.