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

doi:10.1186/1471-2105-5-19

BMC Bioinformatics

Volume 5

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Datta M
Kajdacsy-Balla A
Melamed J
Orenstein J
Dobbin K
Patel A
Dhir R
Becich MJ

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Datta M
Kajdacsy-Balla A
Melamed J
Orenstein J
Dobbin K
Patel A
Dhir R
Becich MJ
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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

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

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

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

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

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

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

author email corresponding author email

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


Published:	27 February 2004

Additional files

Additional File 1:

Excel to XML converting script. Opener7.pl is a Perl script that converts an Excel file to XML-tagged data elements that can be easily inserted into an XML file. This script only works under Windows and requires an installed version of Excel. It is distributed as an open access plain-text file.

Format: PL Size: 3KB Download file

Additional File 2:

CPCTR tissue microarray database file. Cpctrtma.xml is the XML representation of the CPCTR prostate cancer TMA. This file conforms to the TMA Data Exchange Specification and can be viewed as a formatted XML file on most web browsers. The file exceeds 700 KB in length.

Format: XML Size: 773KB Download file

Additional File 3:

TMA validating script. Validtma.pl is a validating Perl script distributed as a plain-text file. It parses through XML files and determines conformance to the TMA Data Exchange Specification [8]. This is an open access Perl script, and is identical to the Perl script distributed with the Specification.

Format: PL Size: 9KB Download file