Institute for Advanced Biosciences, Keio University, Fujisawa, Japan.
PLoS One. 2009 Nov 11;4(11):e7710. doi: 10.1371/journal.pone.0007710.
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.
METHODOLOGY/PRINCIPAL FINDINGS: 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.
CONCLUSIONS/SIGNIFICANCE: 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/).
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重要的背景。因此，在线途径浏览器的可用性将促进后基因组研究，就像基因组浏览器促进了基因组学一样。许多途径图谱已作为公共途径数据库的一部分在线提供。然而，这些图谱中的大多数仅作为特定数据库的网关接口，其代表实体的全面性、数据映射功能和用户界面并不总是足以满足通用用途。
方法/主要发现：我们确定了途径浏览器的五个核心要求：（1）提供显示基因、酶和代谢物的大型综合图谱；（2）全面的搜索功能和数据访问；（3）转录组、蛋白质组和代谢组实验的数据映射，以及编辑和注释途径图谱的能力；（4）途径数据的轻松交换；（5）直观的用户体验，无需安装和定期维护。根据这些要求，我们评估了现有的途径数据库和工具，并实现了一个名为“途径投影仪”的基于网络的途径浏览器作为解决方案。
结论/意义：途径投影仪提供了基于 KEGG 图谱的综合途径图谱，其中增加了基因和酶的节点，并作为利用 Google Maps API 的可扩展、可缩放地图实现。用户可以使用关键字、分子量、核苷酸序列和氨基酸序列，或化合物之间的可能途径，搜索与途径相关的数据。此外，转录组、蛋白质组和代谢组分析的实验数据可以轻松映射。学术用户可免费在（http://www.g-language.org/PathwayProjector/）获得途径投影仪。
