Knowledge Management - Ontologies

Chemistry has a bit of background in ontologies, and ChemAxiom is certainly not the first (though I think it is rather promising…). Three years ago I gave a presentation at the CUBIC (now existing as LinkedIn Alumni Group), which is not so extensive, but does have a few interesting citations on the use of ontologies in chemistry on slide 16:

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Bioclipse for CDK Developers #2

I reported earlier how Bioclipse allows you to use a script to perceive atom types for the content of the JChemPaint RCP editor. This functionality is now available in the outline, and indicates directly if Bioclipse (and the underlying CDK) understands the chemistry you are drawing. In a future Bioclipse release, these problems will be visualized more prominently, likely using the Errors/Problems Views available from Eclipse, or otherwise.

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Making patches; Attribution; Copyright and License.

I have discussed this in the past on mailing lists, but realized yesterday that I need to strengthen the message a bit more. Just to remove confusion. The below is extracted from an email I sent this morning to the cdk-user mailing list, but I’m sure you can apply this to any other open source project. (Disclaimer: I have not studied international law, and the below cannot be used as legal advice. Like you would have! Hahahaha! Let it be pointers :)

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JChemPaint hack session at Uppsala

Arvid and I had a meeting on the ControllerHub refactoring, to make it modular to the bone. Actually, it is the IChemModelRelay that needs refactoring. This is what we wrote down:

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Michel Dumontier at Uppsala University

Michel visits our group this week and gave a very exciting talk yesterday on the role of ontologies in drug discover. This being ongoing research in our group too, the talk was well received by the audience (which was not too large, because after mid-summer, Uppsala has holiday). First the first time, I microblogged a talk on my twitter account (using the #dumontieratuppsala tag). I have not got a XSLT ready to convert the relevant items into a nice HTML snippet for embedding in this blog, but will try to do that later. Meanwhile, I also made a few bookmarks here and there, which are available from Delicious.

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The Dr Who's of Life Sciences

Peter recently wrote up a model of how several Blue Obelisk (please contribute to the page!) projects changed in history: The Doctor Who Model of Open Source. This was later picked up by Glyn and then by Slashdot (second time Peter got that fame; that’s one of the advantages of working at a well-known institute, instead of something like Uppsala University. Beside Bioclipse, GROMACS and the CDK, MySQL AB actually has a headquarters here.) Thanx to Chris who pointed me to the Slashdot coverage.

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Bioclipse-JChemPaint

The Uppsala and EBI CDK-teams have been working hard on finishing the rewrite of JChemPaint I started with Niels earlier. While the EBI-team focused on the applet (and Swing application), the Uppsala team, obviously, focused on the SWT side, for integration into Bioclipse. The new JChemPaint is reaching a useful state, and below is a quick update screenshot something Arvid has been working on:

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