chem-bla-ics

Rich recently blogged about the limitations of the two-atom bond representation often used in chemoinformatics, triggered by the four ferrocene entries in PubChem. In reply to himself, Rich described FlexMol, an XML language that can describe bond systems that involve more than two atoms.

Obviously, the problems originates from the lack of mathematical knowledge of chemists: the current chemoinformatics heavily depends on graph theory, where each atom is a vertex and each bond an edge. This has the advantage that we can borrow all algorithms that work with graph representations, such as Dijkstra's algorithm to find the shortest path between two vertices. Or, in chemical language, an algorithm to calculate how many bonds two atoms are apart in a molecule.

Last night I upgraded the software behind Chemical blogspace, to the version online on Google Code, though I needed the help from Eaun to get paper titles correctly picked up for ACS journals. The number of working blogs is a bit down and now at 68, with an average number of 30 active blogs posting more than 100 blog items each day (see Zeitgeist).

Update: check these two papers.

We all know the combinatorial explosion when calculating the number of possible constitutional isomers (see wp:structural isomorphism) of a certain molecular formula. For example, C2H6 has only one constitutional isomer (ethane, InChI=1/C2H6/c1-2/h1-2H3), and C4H10 has only two. Especially, breaking symmetry by replacing one carbon by another element, or replacing a single by a double bond, increases the number sharply.

I just found out that a review article that I wrote earlier this year got printed: Molecular Chemometrics (DOI: 10.1080/10408340600969601), with my personal view on the interplay between chemoinformatics and chemometrics. The review discusses interesting developments in the last five years, and was fun writing (reading too, I think :).

Peter blogged about the h-index, which is a measure for ones scientific impact. He used Google Scholar, but I do not feel that that database is clean enough. I believe a better source would be the ISI Web-of-Science.

Therefore, I composed a list of h-indices of my own, ordered by value.

Because no one picked up my Chemo::Blogs suggestion, I will now officially claim the blog series title. However, unlike the original Bio::Blogs series, I will not summarize interesting blogs, but just spam you with websites I recently marked as toblog on del.icio.us.

Semantics and Text Mining

Evan Prodromou wrote about RDFa vs microformats. The latter are commonly used in enhancing blog semantics, and for example used by PostGenomic.com. While RDFa is more explicit, e.g.

Contributions to open data do not have to be large, as long as many people are doing it. The Wikipedia is a good example, and PubChem accepts contributions of small databases too (I think). The result can still be large and rather useful, even scientifically.

The latter was recently written down in the paper Internet-based monitoring of influenza-like illness (ILI) in the general population of the Netherlands during the 2003–2004 influenza season by Marquet et al. (DOI: 1471-2458/6/242).