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Sunday, November 22, 2015

WikiPathways: capturing the full diversity of pathway knowledge

Figure from the new NAR paper.
Biology is a complex matter. The biological matter indeed involves many different chemicals in very many temporospatial forms: small compounds may be present in different charge states (proteins too, of course), tautomers, etc. Proteins may exhibit isoforms, various post-translational modifications, etc. Genes shows structures we are only now starting to see: the complex structures in the nucleus have been invisible to mankind until some time ago. Likewise, the biological processes, encoded as pathways, cover an equal amount of complexity.

WikiPathways is a community run pathway database, similar to others like KEGG, Reactome, and many others. One striking difference is the community approach of WikiPathways: anyone can work on or extend the content of the database. This makes WikiPathways exciting to me: it encodes very different bits of biological knowledge, and a key reason why I joined Chris Evelo's team almost four years ago. Importantly, this community is supported by a lively and reasonably sized (>10 people and growing) curation team, primarily located at Maastricht University and the Gladstone Institutes.

The newest paper in NAR (doi:10.1093/nar/gkv1024) outlines some recent developments and the growth of the database. There is still so much to do, and given the current speed at which we learn new biological patterns, this will not get less soon.

Want to help? Sign up, enlist your ORCID! Need ideas what you can do? Why not take a recent paper you published (or read), take a new biological insight, look up an appropriate pathway and add that paper. If you have a novel pathway or important new insight in a biological paper published, why not convert that figure from that paper into a machine readable pathway?

Kutmon, M., Riutta, A., Nunes, N., Hanspers, K., Willighagen, E. L., Bohler, A., Mélius, J., Waagmeester, A., Sinha, S. R., Miller, R., Coort, S. L., Cirillo, E., Smeets, B., Evelo, C. T., Pico, A. R., Oct. 2015. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research. http://dx.doi.org/10.1093/nar/gkv1024