DBPedia enters rdf.openmolecules.net

As of tonight, rdf.openmolecules.net links to the chemistry DBPedia (1816 chemical compounds), for which I used the SPARQL given in DBPedia: lookup and autocomplete of chemistry. It’s first of several steps to extend rdf.openmolecules.net to link up various chemistry database. The below figure shows the current state, where the green nodes are fully RDF-ied:

less than 1 minute read

Bioclipse for CDK Developers #1

Ola has released the second beta for Bioclipse 2.0. Things are getting along, and I will not go into details on the molecules table Arvid is working on, the 1GB+ SD file support, the validating CML editor, the support for XMPP services, or the brand new welcome page which will guide new users around in what Bioclipse has to offer.

3 minute read

Blogger Degrading...

Did others notice this too? The blogger.com Links to this post functionality seems seriously broken… once a rather useful feature, it has now degradated to a useless state:

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DBPedia: lookup and autocomplete of chemistry

On the DBPedia discussion mailing list there was a post on a nice web page which allows you to look up things, and which features a autocomplete edit field. The below screenshot show lookup of molecular structures:

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CDK 1.2 Release Candidate

I released CDK 1.1.5 today. Below is the email I sent to the cdk-user mailing list:

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Where can I host my experimental data? Open Submission Chemistry Databases #1

Rich just posted an interesting read on Web-Centric Science, after a gauntlet thrown down by The Realm of Organic Synthesis (TROS).

1 minute read

Why can't SourceForge just remember me?

I do not typically make complaints in my blog, so consider this a request for advice in good practices ;)

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