The Reactome pathway browser has long been a favorite of ours. We’ve watched it evolve over the years, and continue to appreciate the organization and features that it provides for exploring pathways and interactions across a range of species.
From the mailing list recently, I learned about a new version of the Reactome Pathway Portal, v3.0, that’s now available for everyone. I’ll post a piece of it here, but you can click through to their announcement for full details.
The Reactome team announces the release of our new pathway browser, accessible through our web site http://www.reactome.org/PathwayBrowser/ . The browser provides faster and more reliable navigation of our content and better access to our analysis tools. Improvements include improved and customizable color schemes, and the ability to search for terms within an individual pathway diagram using names, gene names and identifiers including identifiers for molecules hidden within complexes and molecule sets displayed in the diagram. The browser “back” and “forward” buttons allow the user to review every selection made to reach the current view. The level of detail shown in diagrams is zoom-dependent, so recurring small molecules like ATP and water fade out and colored overlays appear to identify subpathways appear as the user zooms out, providing a more legible and informative overview.
So their great foundation remains, but navigation is improved and other features have changed in this update. Delightfully, they have created a short intro video as well, and that becomes our Video Tip of the Week today. Note: there’s no audio with this, watch for the annotations.
I expect that there will be a paper to come with the new details, but I wasn’t able to locate it just yet. I’ll add back the reference when I find it (and yes, I do trawl the Advance Access section of NAR to see what’s coming in the next database issue pretty regularly….).
Reactome main site: http://www.reactome.org
Reactome new pathway browser: http://www.reactome.org/PathwayBrowser
Croft, D., Mundo, A., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M., Jassal, B., Jupe, S., Matthews, L., May, B., Palatnik, S., Rothfels, K., Shamovsky, V., Song, H., Williams, M., Birney, E., Hermjakob, H., Stein, L., & D’Eustachio, P. (2013). The Reactome pathway knowledgebase Nucleic Acids Research, 42 (D1) DOI: 10.1093/nar/gkt1102