The tissue micro-array data exchange specification: a web based experience browsing imported data.
The tissue micro-array data exchange specification: a web based experience browsing imported data.
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DOI：
10.1186/1472-6947-5-25
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发表时间：
2005-08-08
影响因子：
3.5
通讯作者：
Ayers LW
中科院分区：
文献类型：
--
作者：
Nohle DG;Hackman BA;Ayers LW
艾滋病和癌症标本资源（ACSR）是由美国国家癌症研究所（NCI）癌症治疗和诊断部门（DCTD）赞助的艾滋病毒/艾滋病组织库联盟。ACSR向批准的研究人员提供HIV感染的生物样本和未感染的对照组织，包括微阵列（TMA）中的组织核心以及去识别的临床数据。对TMA组织核心的类型和质量以及相关临床数据感兴趣的研究人员需要一种有效的方法来查看可用的TMA材料。因为TMA内的每个组织样本具有单独的数据，包括核心组织数字图像和临床数据，所以需要有组织的标准方法来产生、导航和发布这样的数据。病理学信息学协会（API）于2003年4月提出的可扩展标记语言（XML）TMA数据交换规范（TMA DES）为TMA数据提供了通用格式。将TMA数据导出为建议的格式提供了实现API TMA DES的机会。使用我们的公共BrowseTMA工具，我们创建了一个网站，为研究人员组织和交叉引用TMA列表，数字“虚拟幻灯片”图像，TMA DES导出数据，链接图例和临床细节。Microsoft Excel®和Microsoft Word®用于转换表格式临床数据并生成TMA DES格式的XML文件。BrowseTMA工具包含可扩展样式表语言转换（Extensible Stylidation Language Transformation，缩写EML）脚本，可将XML数据转换为超文本标记语言（Hypertext Mark-up Language，缩写HTML）网页，并自动添加超链接以实现快速导航。在ACSR网站上提供了14个组织块的组织块列表、虚拟载玻片图像、图例、临床详细信息和导出，其中1623个组织块的芯尺寸为2.0、1.0和0.6 mm。我们的虚拟显微镜可用于查看和注释这些TMA图像。研究人员可以很容易地从TMA块列表导航到TMA图例和选定组织核心的临床细节。使用BrowseTMA工具处理了来自其他三个机构的11个区块的3812个核心的出口。使用了TMA DES中的50个通用数据元素（CDE），并为站点特定数据创建了42个通用数据元素。研究人员可以下载TMA DES格式的TMA临床数据。感兴趣的研究人员可以使用BrowseTMA工具在互联网上查看带有临床数据的虚拟TMA。我们已经组织了我们的方法来制作，分类，导航和发布TMA信息，以促进此类审查。我们将Excel TMA数据转换为TMA DES XML，并将其和来自另一个机构的TMA DES XML导入BrowseTMA，以生成允许我们浏览合并数据的网页。我们提出了增强TMA DES作为这一经验的结果。由于使用了从几个机构导出的数据，我们对API TMA DES进行了改进。为API TMA DES编写了文档类型定义（可选地包括建议的增强）。可以使用独立的验证器来根据DTD检查导出（有或没有建议的增强）。将组织核心图像与易于导航的临床数据相关联，极大地提高了TMA的价值。
The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA.