Molecules in Wikipedia without InChIs

I reported last week about the Molecules in Wikipedia and the plethora of templates used. Chemical blogspace has also been using Wikipedia URLs as molecular identifier and extracting InChIs from the wiki pages (see Using Wikipedia to recognize Molecules in Blogspace ). Several people have shown interest in adding InChIs for molecules in Wikipedia, so here’s a new version of a list it molecules without InChIs:

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Molecules in Wikipedia

I do not care about physical and chemical properties in Wikipedia, as I can easily extract them from other sources. The main value of Wikipedia for molecules is, I think, that it describes the history of a molecule. Additionally, the Wikipedia URL is a nice unique molecular identifier (for example http://en.wikipedia.org/wiki/Lactose) given certain conditions, and many bloggers are using it as such . But, it only is a useful identifier if one (and only one) InChI is stated on the wiki page.

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Excel messes up your data analysis :)

Well, no wonder: Excel is meant to be used to process money flows. Anyway, greyarea pointed me to this nice blog item from March 2006. It discusses a 2004 article in BMC Bioinformatics Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics by Barry Zeeberg et al. (DOI:10.1186/1471-2105-5-80). Hence, the importance of semantics and proper markup languages. The quotes are illustrative:

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RDF-ing molecular space

RDF might be the solution we are looking for to get a grip on the huge amount of information we are facing. microformats, and RDFa, are just solutions along the way, and Gleaning Resource Descriptions from Dialects of Languages (GRDDL) might be an important tool to get the web RDF-ied.

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Further Bioclipse QSAR functionality development

I had some time to work some more on the QSAR functionality in Bioclipse. There is still much to do, but it is getting there. The calculation of a QSAR descriptor data matrix

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OSRA: GPL-ed molecule drawing to SMILES convertor

Igor wrote a message to the CCL mailing list about OSRA:

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Screencasts for life science informatics

Deepak blogged about screencasting for bio topics, concentrated at bioscreencast.com of which he is co-owner. I guess it is like a YouTube for bioinformatics thingies. Jean-Claude picked this up very quickly (seen on Cb? At least I did.), and already uploaded a screencast, demoing JSpecView written by Robert. I wonder if he will upload the screencasts he made for Bioclipse too? (hint, hint … :)

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