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

Berman JJ, Datta M, Kajdacsy-Balla A, Melamed J, Orenstein J, Dobbin K, Patel A, Dhir R, Becich MJ - BMC Bioinformatics (2004)

Bottom Line: TMAs have been used successfully to validate candidate molecules discovered in gene array experiments.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA. bermanj@mail.nih.gov

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.

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Related in: MedlinePlus

Validation script output. Image displaying the interaction between Perl validating script and user.
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Figure 7: Validation script output. Image displaying the interaction between Perl validating script and user.

Mentions: Once a TMA database is prepared, it needs to be validated to ensure conformance with the Specification. At this time, all TMA files should be validated using a software implementation written in Perl and distributed as an open access supplemental file with the Specification and with this publication [see Additional file 3]. The validating script requires a Perl installation but should operate equally well on any operating system. The validation software has a simple command-line interface. When the file successfully validates, the Perl script outputs the encountered CDEs from the Specification, a statement that the file is valid, and a one-way hash value specific for the validated file [see Figure 7].


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

Berman JJ, Datta M, Kajdacsy-Balla A, Melamed J, Orenstein J, Dobbin K, Patel A, Dhir R, Becich MJ - BMC Bioinformatics (2004)

Validation script output. Image displaying the interaction between Perl validating script and user.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC373442&req=5

Figure 7: Validation script output. Image displaying the interaction between Perl validating script and user.
Mentions: Once a TMA database is prepared, it needs to be validated to ensure conformance with the Specification. At this time, all TMA files should be validated using a software implementation written in Perl and distributed as an open access supplemental file with the Specification and with this publication [see Additional file 3]. The validating script requires a Perl installation but should operate equally well on any operating system. The validation software has a simple command-line interface. When the file successfully validates, the Perl script outputs the encountered CDEs from the Specification, a statement that the file is valid, and a one-way hash value specific for the validated file [see Figure 7].

Bottom Line: TMAs have been used successfully to validate candidate molecules discovered in gene array experiments.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA. bermanj@mail.nih.gov

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.

Show MeSH
Related in: MedlinePlus