The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
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DOI：
10.1186/1471-2105-5-19
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发表时间：
2004-02-27
影响因子：
3
通讯作者：
Becich, MJ
中科院分区：
文献类型：
--
作者：
Berman, JJ;Datta, M;Becich, MJ
背景资料：组织微阵列（Tissue Microarrays，TMAs）已成为一种强有力的工具，可用于检测单个载玻片上显示的数百种不同组织中标记分子的分布。TMA已成功地用于验证基因阵列实验中发现的候选分子。像基因表达研究一样，TMA实验是数据密集型的，需要大量的信息来解释，复制或验证。最近，一个开放存取的组织微阵列数据交换规范已经发布，允许TMA数据被组织在一个自我描述的XML文档注释定义良好的共同数据元素。虽然本说明书提供了足够的信息，供外部研究小组复制实验，但其最初的描述并不包含实际实施的说明或示例，也没有发布实施研究。本文的目的是演示如何实现的TMA数据交换规范在前列腺癌TMA.Results：合作的前列腺癌组织资源（CPCTR）是由美国国家癌症研究所资助，为研究人员提供样本的前列腺癌注释人口统计和临床数据。CPCTR现在提供前列腺癌TMA，并实施了符合新的开放获取组织微阵列数据交换规范的TMA数据库。TMA数据库的大部分由299例患者样本的临床和人口统计学数据元素组成。这些数据元素是使用转换Perl脚本从Excel数据库中提取的。Perl脚本和TMA数据库是开放获取的文件，分发与此手稿。结论：TMA数据库符合组织微阵列数据交换规范可以与其他TMA文件合并，通过增加数据元素扩展，或链接到外部生物数据库中包含的数据。本文描述了TMA数据交换规范的开放存取实现，并为希望使用该规范的研究人员提供了详细的指导。
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.