“Pathway diagrams are the road maps of biology.” This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announced. The NAR database issue in January and the mid-year web server issue are perfectly timed items that I can content mine all year ’round. And I am always drawn to the tools which are offering better visualizations for data. PathWhiz is offering better road maps. So I definitely wanted to take a look.
They note that historically pathway data has been artistically rendered for print applications like papers and posters, and can be quite engaging and attractive. But actually working with pathways in computational settings can be a bit more, um, sterile–I guess I would characterize it. Their goal seems to be to merge the two: better options for graphical components, but still machine-readable for further manipulation and exploration. They summarize their goal in this hybrid approach:
PathWhiz is essentially a web server designed for the facile creation of colourful, visually pleasing and biologically accurate pathway diagrams that are machine-readable, interactive and fully web compatible.
The paper goes on to describe a lot of the foundational concepts and the implementation. There are important technical aspects covered about the formats and file types. But the best way to get a feeling for it is their intro video. You can also access that on their tutorial page and I’ll include it here.
Mid-way through this PathWhiz video 1, they show you the difference between a KEGG, Reactome, and WikiPathways visualization to give you a sense of the differences. (~4:15). A part II video is coming,
but not available yet. It has posted since I started this.
Look through the “legends” area to see the kind of handy diagrams you might need–molecules, membranes, or cellular organelles, or even tissues like brain or liver. Tab through the different types of graphics that are available to get a sense of how your pathways could look rendered in the PathWhiz system. You can try it out easily too: there’s a “guest” mode where you can just kick the tires. Or you can create a login and work on some of the ones that might be useful for your work and your presentations and papers. Those can be saved and locked, but can also be cloned and expanded on by other people. You can also get a sense of what some of the more mature diagrams can look like by browsing the pathway collection. I thought this one: 17-alpha-hydroxylase deficiency (CYP17), had nice examples of the tissue (kidney) and organelles involved that quickly give you a grasp of what’s going on and where. I’ve just shown a small part of it in this image, it’s much more detailed at full size. You can zoom in to see the pathway components. And you can see from here that the details are exportable in a number of ways by clicking the “Downloads” tab.
So for better representations for humans to view, while also preserving the important functions that computational renderings can offer, PathWhiz is worth a look. Go over and try it out.
PathWhiz legends to see the graphics: http://smpdb.ca/pathwhiz/legend
Pon, A., Jewison, T., Su, Y., Liang, Y., Knox, C., Maciejewski, A., Wilson, M., & Wishart, D. (2015). Pathways with PathWhiz Nucleic Acids Research, 43 (W1) DOI: 10.1093/nar/gkv399
Benson G (2015). Editorial: annual Web Server Issue in 2015 Nucleic Acids Research, 43 (W1) DOI: 10.1093/nar/gkv581