The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
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DOI：
10.1186/1471-2105-8-456
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发表时间：
2007-11-19
影响因子：
3
通讯作者：
Baliga NS
中科院分区：
文献类型：
--
作者：
Bare JC;Shannon PT;Schmid AK;Baliga NS
万维网上的信息资源在现代生物学中起着不可或缺的作用。但是，由于需要重新格式化数据文件、在命名系统之间进行转换或对公共数据库的本地副本进行持续维护，集成来自多个数据源的数据常常受到阻碍。由于越来越多地使用web协议来传输结构化数据，因此出现了组合和重用数据的新方法。Firegoose是Mozilla Firefox浏览器的扩展，可以在网站和桌面工具之间传输数据。作为Gaggle集成框架的一个组件，Firegoose还可以与Cytoscape、R统计包、Multiexperiment Viewer （MeV）和其他一些流行的桌面软件工具交换数据。Firegoose增加了轻松使用本地数据查询KEGG， EMBL STRING， DAVID和其他广泛使用的生物信息学网站的功能。只需点击几下，这些网站的查询结果就可以转移到桌面工具进行进一步分析。Firegoose通过屏幕抓取、微格式、嵌入式XML或web服务从web获取数据。我们定义了一种微格式，它允许在HTML文档中嵌入与Gaggle兼容的结构化信息。我们通过对微生物盐盐杆菌NRC-1在厌氧环境下激活的基因进行分析，证明了该软件的功能。从微阵列数据开始，我们通过结合来自多个公共网络资源的数据来探索差异表达基因的功能，并构建了所涉及的细胞过程的集成视图。Firegoose将Mozilla Firefox集成到Gaggle环境中，可以在不同的web资源和桌面软件工具之间进行交互式数据共享，而无需维护本地副本。使用Firefox浏览器的脚本平台，可以轻松地将其他网站合并到框架中。在浏览器中执行数据集成，可以将浏览器出色的搜索和导航功能与强大的桌面工具结合使用。
Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.
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影响因子：
14.9
作者：
von Mering C;Jensen LJ;Kuhn M;Chaffron S;Doerks T;Krüger B;Snel B;Bork P
通讯作者：
Bork P
影响因子：
14.9
作者：
Hull D;Wolstencroft K;Stevens R;Goble C;Pocock MR;Li P;Oinn T
通讯作者：
Oinn T
DOI：
10.1073/pnas.190337797
发表时间：
2000-10-24
影响因子：
11.1
作者：
Ng, WV;Kennedy, SP;DasSarma, S
通讯作者：
DasSarma, S
影响因子：
7
作者：
Schmid, Amy K.;Reiss, David J.;Baliga, Nitin S.
通讯作者：
Baliga, Nitin S.
影响因子：
2.7
作者：
Saeed, AI;Sharov, V;Quackenbush, J
通讯作者：
Quackenbush, J