Bioclipse: a powerful Jmol application

While Bioclipse is much more, it could be an interesting alternative to the Jmol application. It offers:

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Open NMR data: raw curves and annotated peak lists

Games are known to trigger technical innovation. But recently it also triggered innovation on open chemical databases. Jean-Claude reported:

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Open Data versus Capatalism?

Ian Davis was recently quoted saying open data is more important than open source, which was pulled (out of context) from this presentation. The context was (a slide earlier): Data outlasts code.

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Solubility Data in Bioclipse #4: Finding ChEBI IDs (Again, but better)

Those who carefully analyzed the second SPARQL query in Solubility Data in Bioclipse #3: Finding ChEBI IDs will have noticed the use of owl:sameAs. Those who did not, here’s the query again:

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Solubility Data in Bioclipse #3: Finding ChEBI IDs

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

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RDF for chemistry

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. It nicely coincides with Rich’ blog on What the Heck is the Semantic Web?, and the RDF work I have recently done on rdf.openmolecules.net and Bioclipse. (Oh, do I wish I could have attended that conference.)

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Solubility Data in Bioclipse #2: handling RDF

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, …).

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