Reactome is an open source, online knowledge base and map of biological processes in humans, including basic metabolism, hormonal signalling, and the cellular pathways that make infection possible. The Reactome map includes sections for each of the 23 processes it currently covers; the arrangement of reactions is reminiscent of a map of constellations, giving the map the nickname "starry sky." Late last month, the Reactome group released the newest version of the map, including for the first time the Influenza and HIV infection cycles -- as well as an entirely new way of visualizing the biological reactions.
[Reactome] is intended to teach scientists about parts of the influenza lifecycle they might not be familiar with, and to help researchers look at specific reactions and figure out ways to block them. [...] The influenza pathway component and a simultaneous HIV database going online mark the first time Reactome has displayed interactions between an infectious pathogen and its host, Dr. Scheuermann said.
Pathogens such as influenza have evolved to use hosts to promote their growth, while at the same time blocking the host reactions that recognize and respond to infection. Each year, for example, winter is marked by the outbreak of flu caused by new viruses that the human immune system doesn't recognize.
The "starry sky" approach is intentional. The various processes and reactions presented by Reactome are often related, and the constellation mapping provides a visualization of those relationships. The Reactome group has found that biomedical researchers can be surprised by the connection of pathways, and the added insights that come from seeing the larger physiological context has proven useful for the development of new treatments.
As noted above, Reactome is open source, and the entire Reactome database (in MySQL), as well as a variety of sub-sections and datasets, can be downloaded freely.
Reactome is very clearly intended for a specialized audience, not a general audience, but the combination of a novel interface that reveals unexpected relationships as well as an open source model for both the underlying data and the site code, definitely mark this as a WorldChanging scientific tool.
(Via Medgadget)
Comments (2)
As a research scientist working in signal transduction/ regulation, this sort of website provides the kind of fingertip knowledge that is enormously useful. Of the several hundred papers that are key references, it is refreshing to see them pared down to the key discoveries, what they actually mean (in biological ssystems) and species specific maps that are created. This sort of thing leads to revolutions in application of accumulated knowledge. Considering that hundred to thousands of papers are published in apoptosis research alone, this is an enormous aid in filtering the information stream.
But what is saddening is that I have not heard of this website via my research channels. WorldChanging is rapidly becoming my major source for innovative ideas and sources of new information. This strongly implies that the traditional channels of communication in the scientific community are slow and (maybe) wary of straying from their traditional disciplines (i.e.- biology and computer science).
Keep up the good work guys!
Posted by Xavier | February 7, 2006 4:33 PM
Posted on February 7, 2006 16:33
I'm glad we can be of service, Xavier!
Posted by Jamais Cascio | February 7, 2006 8:28 PM
Posted on February 7, 2006 20:28