Li Feng, Li Maoyu, Xiao Zhiqiang, Zhang Pengfei, Li Jianling, Chen Zhuchu
Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China.
BMC Bioinformatics. 2006 Jan 11;7:13. doi: 10.1186/1471-2105-7-13.
Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database.
The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database.
Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.
许多蛋白质组学计划要求从样本采集、数据展示到实验结果发表，以统一标准整合所有信息。整合和交换这些格式与结构各异的数据给我们带来了巨大挑战。XML技术因其简单性和灵活性，有望处理这项任务。鼻咽癌（NPC）是中国南方和东南亚最常见的癌症之一，其发病率在地理和种族上存在显著差异。尽管现在有一些癌症蛋白质组数据库，但仍没有鼻咽癌蛋白质组数据库。
鼻咽癌蛋白质组实验原始数据通过人类蛋白质组标记语言（HUP-ML）编辑器捕获到一个XML文档中，并导入到原生XML数据库Xindice中。利用Apache、PHP和Xindice构建了鼻咽癌蛋白质组的二维/质谱库，以便通过互联网访问该数据库。在我们的网站上，同时提供了关键词查询和点击查询两种方法来访问鼻咽癌蛋白质组数据库的条目。
我们的二维/质谱库可用于共享基于凝胶的蛋白质组学实验产生的鼻咽癌原始蛋白质组学数据。该数据库以及构建用户自己蛋白质组库的PHP源代码可在http://www.xyproteomics.org/上获取。
