Citing the Chemistry Development Kit

Two weeks ago, a paper by Peter Ertl was published about Molecular structure input on the web (doi:10.1186/1758-2946-2-1). In this paper, he discusses the state of things and describes his contribution to this field, the JME Molecule Editor. The article also cites the CDK, but only the website and not one of the two papers (doi:10.1021/ci025584y, or doi:10.2174/138161206777585274). This is not an isolated case, but a common pattern. In principle, the proper work is cited, and nothing is wrong. Practically it means, that a citation to the CDK website does not show up in the citation network. This is not a problem caused by these papers, but merely by the nature current citation databases work: they only count citations between journal articles, and only sometimes extend to books or conference abstracts.

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Google Scholar allows downloading as BibTeX

 

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JChemPaint in OpenOffice.org! Cheers to Konstantin!

 

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Bioclipse understands ontologies: note how the InChI is not part of the RDF graph

 

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ChEMBL RDF #1:SPARQL end point

In a series of SPARQL end points, I am happy to present a new Virtuoso 6.1-hosted SPARQL end point for the ChEMBL database (CC-BY-SA), at our groups new rdf.farmbio.uu.se server. The server is hosting 23.8M triples, with the data based on ChEMBL 02. There is a SPARQL end point, as well as a SNORQL interface:

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RDF, Jena, Bioclipse, Eclipse, Zest: Mashups

Quite a while a go, I blogged about Zest in Bioclipse showing a bit of ONS Solubility data. I could not follow up on that until now, as I had yet to do a lot of RDF work in Bioclipse, so the screenshot back then was kind of a mockup.

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Average time on Site: chem-bla-ics

Cameron freeded(?) on the Spanish and Dutch sticking around longest on his site. I’ve never used Google Analytics for that, but it’s good time spent on procrastination: it makes nice graphics:

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