Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video: It’s a really nifty piece of work, which goes into the differences between thesauri, controlled vocabularies, and, as such, ontologies, and social tagging systems. Both have their virtues; it is fuzzy logic versus ODEs all over again. Whether one is better than the other only depends on the problem at hand.
I was pleased to hear that Christoph will move to the EBI early next year. Christoph has been working on Open Source and Open Data chemoinformatics since at least 1997. I first got in contact with Christoph when I wrote code for JChemPaint (which Christoph developed) to be able to read Chemical Markup Languages (CML). This also got me into contact with Dan Gezelter who is the original author of Jmol, to which I also added CML support.
As promised , here is my list of submission for the Open Laboratory 2007: Open Data is critical for Reproducible Research If you ever made something fluoresce after you did a reaction with a transition metal… One For the Brave Fun with singlet oxygen SMILES and Aromaticity: Broken?
Chemistry World December issue features a nice item on the future of data in chemistry: Surfing Web2O; Peter gave an excerpt, and Peter commented on it . The article discusses many of the things that have been happening in the field of chemical data. It touches Jean-Claude’s work on Open Notebook Science, and then moves to Peter’s Open Data, mentions a number of other blogs and the Chemical blogspace.
I recently saw that blogger.com blogs gained a poll feature. From now on, I will try to be a bit more Open Science, in addition to Open Source. From now on, you can be in my Advisory Board. To do so, vote on my next chemblaics (aka Open Source Chemoinformatics) project. The poll can be found on the left side of this blog.
My current jobs description is to speed up metabolomics data analysis, and finally got around to making a first relevant workflow for Taverna, using the webservices just posted over at ChemSpider: I uploaded the source to MyExperiment, so anyway can play with it. There is much to improve, such as using CDK-Taverna for further analysis of the results.
The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.
Jim shows that some people do not think webservices standards are complex enough in itself:
During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg. The package provides GA support for binary and real-value chromosomes (and integer chromosomes is something that will be added soon), and allows to use custom evaluation functions.
Third in the series of blogs about molecules in Wikipedia without an InChI (see also #1 and #2 ). There a certainly false positives, but here’s the updated list: http://www.en.wikipedia.org/wiki/AZD2171 http://www.en.wikipedia.org/wiki/Alizarin http://www.en.wikipedia.org/wiki/Allantoin http://www.en.wikipedia.org/wiki/Allylamine http://www.en.wikipedia.org/wiki/Alpha-ethyltryptamine http://www.en.wikipedia.org/wiki/Anthraquinone
Pedro reminded me of the last call for Open Laboratory 2007, which prints the best blog items of 2007 in book form. The list of chemistry contributions is not so large yet, so go ahead and nominate some of cool chemical blog items of the last year. I will post my shortlist later this week.