Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
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DOI：
10.1371/journal.pone.0007710
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发表时间：
2009-11-11
期刊：
影响因子：
3.7
通讯作者：
Tomita M
中科院分区：
文献类型：
--
作者：
Kono N;Arakawa K;Ogawa R;Kido N;Oshita K;Ikegami K;Tamaki S;Tomita M
生化途径为理解全面的实验数据和细胞的系统工作提供了必要的背景。因此，在线路径浏览器的可用性将促进后基因组研究，就像基因组浏览器对基因组学的贡献一样。许多路径图已经作为公共路径数据库的一部分在线提供。然而，这些映射中的大多数都充当到特定数据库的网关接口，它们所表示的实体、数据映射功能和用户界面的全面性并不总是足以用于一般用途。我们已经确定了途径浏览器的五个核心要求：(1)具有显示基因、酶和代谢物的大型集成地图的可用性；(2)全面的搜索功能和数据访问；(3)转录组学、蛋白质组学和代谢组学实验的数据制图，以及编辑和注释通路图的能力；(4)路径数据交换方便；(5)直观的用户体验，无需安装和定期维护。根据这些要求，我们评估了现有的路径数据库和工具，并实施了一个基于网络的路径浏览器，名为路径投影仪作为解决方案。Pathway Projector提供了基于KEGG Atlas的集成路径图，增加了基因和酶的节点，并利用谷歌maps API实现了可缩放的可缩放地图。用户可以使用关键词、分子量、核苷酸序列、氨基酸序列或化合物之间可能的路径来搜索通路相关数据。此外，转录组学、蛋白质组学和代谢组学分析的实验数据可以很容易地绘制。学术用户可以在http://www.g-language.org/PathwayProjector/上免费获得PathwayProjector。
Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at http://www.g-language.org/PathwayProjector/.
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影响因子：
14.9
作者：
Chung HJ;Park CH;Han MR;Lee S;Ohn JH;Kim J;Kim J;Kim JH
通讯作者：
Kim JH
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
DOI：
10.1049/sb:20045008
发表时间：
2004-06-01
期刊：
Systems Biology
影响因子：
--
作者：
Hucka, M.;Finney, A.;Kitano, H.
通讯作者：
Kitano, H.
影响因子：
5.8
作者：
Arakawa, K;Mori, K;Tomita, M
通讯作者：
Tomita, M