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:var ons = rdf.createStore()

// output: RDFStore: 0 triples

rdf.importURL(ons,

"http://github.com/egonw/onssolubility/raw/master/ons.solubility.rdf/ons.rdf")

// output: RDFStore: 1206 triples

var results = rdf.sparql(ons, "PREFIX owl: <http://www.w3.org/2002/07/owl#> " +

"PREFIX ons: <http://spreadsheet.google.com/plwwufp30hfq0udnEmRD1aQ/onto#> " +

"SELECT DISTINCT ?same WHERE { " +

" ?solvent a ons:Solvent .

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.

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, ...).

Yesterday I uploaded a Bioclipse feature that adds a rdf manager to handle RDF content, which includes SPARQL support.
4

This week I have been porting the PubChem plugin for Bioclipse 1.2 to the new manager-based architecture. While still working on the Wizards, you can run the following JavaScript in Bioclipse2 from SVN and from the next beta (*):

*) There was some confusion on the two beta Bioclipse2 releases so far. Some people expected a release without any bugs left. That release is what we planned to call a Release Candidate.
6

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:

Drugs are still missing, but will add those too, and since not all entries had InChIs, SMILES were converted using CDK 1.1.5.
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.

This blog will focus on what Bioclipse has to offer CDK developers.

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:

I'm quite sure a post of last October cannot link to the Substructure searching on ONS solubility data item Jean-Claude posted today.
2

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:

If you are not ware of this, adding content to DBPedia is as easy as adding something to WikiPedia. Literally: DBPedia is the RDF flavour of WikiPedia. It extracts the information from the info boxes, as I discussed before (see Molecules in Wikipedia).
1

I release CDK 1.1.5 today. Below is the email I sent to the cdk-user mailing list:Hi all,

I am happy to be able to announce the first Release Candidate for CDK 1.2.

Everyone using using CDK 1.0 is suggest to upgrade to this release,

which has fewer bugs, is much better tested, and is faster too. It

also comes with API changes, and a full changelog is not available

(yet).
10

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

I agree that this still is a problem: where can (organic) chemists host their data? TROS hints as Wikipedia, but an encyclopedia is not always the most suited place for cutting edge chemistry (article can easily be biased, contain (science) political views, etc...).
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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