The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data.
The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data.
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DOI：
10.1186/1472-6947-3-5
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发表时间：
2003-05-23
影响因子：
3.5
通讯作者：
Friedman, Bruce A
中科院分区：
文献类型：
--
作者：
Berman, Jules J;Edgerton, Mary E;Friedman, Bruce A
背景：组织微阵列（TMAs）允许研究人员在单个载玻片上检查数百个小组织样本。在一张TMA幻灯片中保存的信息可能很容易就涉及到数十亿字节的数据。为了从TMA技术中受益，科学界需要一个开源的TMA数据交换规范，该规范将以人类和计算机都可以理解的格式传输TMA实验中的所有数据。TMA的数据交换规范允许研究人员将他们的数据提交给期刊和公共数据存储库，并共享或合并来自不同实验室的数据。在2001年5月，病理信息学协会（API）主办的第一个系列的四个研讨会，共同主办的国家癌症研究所，开发一个开放的，社区支持的TMA数据交换specification.METHODS：组织微阵列数据交换规范草案通过研讨会会议。第一次研讨会确认了社区对这一努力的支持，并敦促创建一个基于XML的开放规范。这是逐步发展的，在开放研讨会期间，用户社区的利益相关者批准了每一步。到2002年10月举行的第四次研讨会为止，建立了一组公共数据元素（CDE），以及在自描述XML文档中组织TMA数据的基本策略。结果：TMA数据交换规范是一个格式良好的XML文档，具有四个必需的部分：1）标题，包含规范都柏林核心标识符，2）块，描述石蜡包埋的组织阵列，3）载玻片，描述由块产生的载玻片，和4）核心，包含与阵列中包含的各个组织样品相关的所有数据。80个符合ISO-11179数据元素规范的CDE构成了TMA数据交换规范中使用的XML标签。一组六个简单的语义规则描述了完整的数据交换规范。任何使用数据交换规范的人都可以使用Perl编写的软件实现来验证他们的TMA文件，并作为补充文件与本publisher.CONCLUSION一起分发：TMA数据交换规范现在以草案形式提供，包括社区批准的通用数据元素和社区批准的通用文件格式和数据结构。该规范可供科学界自由使用。由病理学信息学协会赞助的完善TMA数据交换规范草案的努力预计将持续至少两年。邀请感兴趣的公众参与这些公开努力。有关未来研讨会的信息将在http://www.pathologyinformatics.org（API网站）上发布。
BACKGROUND: Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification.METHODS: A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents.RESULTS: The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication.CONCLUSION: The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at http://www.pathologyinformatics.org (API we site).