With the RDF functionality set up in Bioclipse (see Solubility Data in Bioclipse #2: handling RDF ), we can start mining the Chemical RDF space.

C-SHALS 2009 (Conference on Semantics in Healthcare and Life Sciences) has just started, and has coverage in a blog and in a FriendFeed room.

RDF is swiftly becoming the lingua franca of life sciences (see for example [1 ,2]). Bioclipse is an excellent platform to visualize results from analysis of the network, both for graph visualization (see [3 ]), as well of visualization of domain specific data types (e.g. sequences, molecules, …).

This week I have been porting the PubChem plugin for Bioclipse 1.2 to the new manager-based architecture.

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.

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.

Did others notice this too?

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.

I released CDK 1.1.5 today.

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

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