A Web Tool for Generating High Quality Machine-readable Biological Pathways

作者：Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, Jason R. Grant, Anthony Yan‐Tang Wu, David S. Wishart · 发表于：Journal of Visualized Experiments · 年份：2017 · DOI：10.3791/54869 · 被引用次数：9 · 研究领域：Bioinformatics and Genomic Networks、Computational Drug Discovery Methods、Cell Image Analysis Techniques

PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate i...