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Tuesday, October 18, 2011

The Blue Obelisk Shoulders for Translational Cheminformatics

I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to developed Open Source-based cheminformatics solutions. I created the following diagram for the paper, showing how various Blue Obelisk projects interoperate (image is CC-BY, from the paper):


It shows a number of Open Standards (diamonds), one Open Data set (rectangles), and Open Source projects (ovals). What does diagram is not showing, is the huge amount of further Open Source cheminformatics projects around, that use one or more of the components listed here, but which do not link themselves to the Blue Obelisk directly. And there are many indeed, both proprietary and Open.

I am proud of this diagram: it really shows that the interoperability we set out in the first paper worked out very well! This makes the Blue Obelisk an excellent set of shoulders to do translational cheminformatics.

Translational cheminformatics?? Well, I have been looking for a while for a good term for my research regarding all that hacking on the CDK, Bioclipse, etc. Now, that's the translation of my core molecular chemometrics research to other scientific fields, like metabolomics, toxicology, etc.

ResearchBlogging.orgGuha, R., Howard, M., Hutchison, G., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. (2006). The Blue Obelisk - Interoperability in Chemical Informatics Journal of Chemical Information and Modeling, 46 (3), 991-998 DOI: 10.1021/ci050400b

ResearchBlogging.orgO'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR, James CA, Jeliazkova N, Lang AS, Langner KM, Lonie DC, Lowe DM, Pansanel J, Pavlov D, Spjuth O, Steinbeck C, Tenderholt AL, Theisen KJ, & Murray-Rust P (2011). Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of cheminformatics, 3 (1), 37 PMID: 21999342 DOI: 10.1186/1758-2946-3-37