A GSoC project idea around the Resource Description Framework

I just added an entry to the Google Summer of Code 2010 Ideas wiki page:

Resource Description Framework (RDF) is ~10 year old W3C standard. Uptake is taking off now, and it would be nice to see a Eclipse project like the Web Tools Package to provide basic RDF related functionality. This would include bundles for RDF libraries (Jena or OpenSesame) and editors for Notation3 and RDF/XML, and perhaps support for a catalog of common ontologies (RDF, RDFS, OWL, DublinCore, FOAF, ...). It could also include a Zest-based RDF graph viewer, SPARQL query editor, etc. There is existing code, for example, developed by the Bioclipse team using Jena, or the older Tripclipse. There also exist commercial offerings stressing the relevance of the RDF platform, such as Semantic Toolkit and the popular TopBraid.

For Bioclipse we have set up bundles for Jena in the bioclipse.rdf git repository, but I am sure they need some improvement. Yet, they might serve as a starting point.

RDF-powered QSAR wizard: SPARQL end points providing wizard content

As you know from my blog, one of the things I am working on is to push RDF functionality in Bioclipse, as I believe it to be the missing link between molecular chemometrics and literature, databases, and other non-numerical information sources.

As part of the submission for the SWAT4LS special issue in the new Journal of Biomedical Semantics, Ola hacked up a cool wizard that sets up a new QSAR Project by downloading data directly from our RDF node for the chEMBL data using SPARQL. The paper is based on the SWAT4LS talk I gave, and the proceedings paper that recently appeared. But with more cool stuff, such as this cool RDF graph browser that allows you to open up molecules from the RDF graph in a JChemPaint editor.

Well, this really nice New QSAR Project wizard was cool enough to trigger a I-want-more reaction, so I just had to hack it up with some additional SPARQL functionality. So, the next version does not only use RDF and SPARQL to aggregate the QSAR data set, it also uses SPARQL to make the wizard interactive. While the user is typing a target ID, the wizard will check the SPARQL end point in the background and download the target's type, title and organism, as well as update the list of activities the user can select depending on what the chEMBL database has for that target:

The actual code base is pretty small, and that's what happens when you mash up the right technologies :)

RDF, Jena, Bioclipse, Eclipse, Zest #2: icons and an extension point

Jonathan worked this week on new features for the Bioclipse RDF editor (see these two earlier items). This version still does not edit, but only display using Zest. Jonathan created for me an extension point so that anyone can make the editor aware of domain objects, by simply registering the extension implementation along with the rdf:Class URI of the rdf:type of an object. This fixes the problem of having to hardcode dependencies of the RDF editor on all the domain code, as was the case earlier.

For example, the cheminformatics IMolecule object is now linked to the rdf:type <http://www.bioclipse.net/structuredb/#Molecule>:

<extension point="net.bioclipse.rdf.rdf2bioobjectfactory">
  <Factory
    instance="net.bioclipse.rdf.ui.RDFToCDKMoleculeFactory"
    uri="http://www.bioclipse.net/structuredb/#Molecule" >
  </Factory>
</extension>

The API for this factory looks like:

public IBioObject rdfToBioObject( Model model, Resource res );
public ImageDescriptor getImageDescriptor();

This is very much tied into the Jena data model, so not entirely clean, but has to do for now. The first method converts RDF content into a Bioclipse IBioObject, such as an IMolecule (see this list of currently supported objects). The second method returns an icon, which makes the editor more visually pleasing, and provides a nice way to see when you can double click the RDF node to have it open in an domain specific editor:

For example, double clicking the ron:mol2 node, would open up a JChemPaint editor.

RDF, Jena, Bioclipse, Eclipse, Zest: Mashups

Quite a while a go, I blogged about Zest in Bioclipse showing a bit of ONS Solubility data. I could not follow up on that until now, as I had yet to do a lot of RDF work in Bioclipse, so the screenshot back then was kind of a mockup.

Things are different now, and the Bioclipse-RDF functionality (using Jena) is released in Bioclipse 2.2 (see Semantic Web features in Bioclipse 2.2), and I got around to writing the graphical goodies for the following papers. Not submitted yet, but here's the screenshot showing a N3 file opened with a Zest-powered editor (read-only) and a plain text editor:

Semantic Web features in Bioclipse 2.2

Ola is releasing Bioclipse 2.2.0 today, and asked me to show case the semantic web functionality in Bioclipse. I realized that I do not have a nice page showing the semantic web overview. But I did blog a lot about RDF functionality, so here's a list of pointers:

• Bioclipse Manager for MyExperiment.org
• Bioclipse, RDF and defeasible reasoning (see also Samuel's blog)
  
• Bioclipse and SPARQL end points #2: MyExperiment
  
• Bioclipse and SPARQL end points
  
• Solubility Data in Bioclipse #2: handling RDF
  
• Solubility Data in Bioclipse #3: Finding ChEBI IDs
  
• Solubility Data in Bioclipse #4: Finding ChEBI IDs (Again, but better)
  
• /me is having Bioclipse/XMPP/RDF fun
  

Or check this screenshot from a Posterous post about a MyExperiment workflow:

One thing I have not blogged about yet (I think), is that the Bioclipse RDF manager also understands RDFa now. Well, sort of... it relies on a webservice, but this is what the script looks like:

model = rdf.createStore()
rdf.importRDFa(model, "http://egonw.github.com/")
rdf.saveRDFN3(model, "/Virtual/egonw.n3")

With support of SPARQL end points, and reading RDF from web resources directly (RDF/XML, N3, RDFa), Bioclipse is ready for the chemical semantic web.

Bioclipse and SPARQL end points

Last week, there was a very interesting thread on the DBPedia mailing list, on using Java for doing remote SPARQL queries. This was one of the features still missing in bioclipse.rdf. Richard Cyganiak replied pointing the code in Jena which conveniently does this and which bioclipse.rdf is already using anyway. Next, Fred Durao even gave a full code example relieving me from any further research, resulting in sparqlRemote() now implemented in the rdf manager:

> rdf.sparqlRemote(
  "http://dbpedia.org/sparql",
  "select distinct ?Concept where{[] a ?Concept } LIMIT 10"
);
[[http://dbpedia.org/ontology/Place], [http://dbpedia.org/ontology/Area],
[http://dbpedia.org/ontology/City], [http://dbpedia.org/ontology/River],
[http://dbpedia.org/ontology/Road], [http://dbpedia.org/ontology/Lake],
[http://dbpedia.org/ontology/LunarCrater],
[http://dbpedia.org/ontology/ShoppingMall], [http://dbpedia.org/ontology/Park],
[http://dbpedia.org/ontology/SiteOfSpecialScientificInterest]]

I reported earlier two example SPARQL queries for chemistry, which can now be rewritten as Bioclipse scripts:

and

Which feature must I install for org.eclipse.zest?

Dear lazyweb!

I have been trying to figure out which Eclipse 3.4 feature I must install from the update site to get the org.eclipse.zest plugin in my environment.

I installed the Zest feature (which I am going to use to visualize an RDF network), but my workspace still complained that I did not have the plugin.

Maybe I should rerun Set Target Platform for our product, but I and others in the Bioclipse development community have been wondering how we can know what feature to install via the Software Updates... to get a particular plugin on your machine?

Looking forward to hearing from you,

Kind regards,

Egon

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, ...).

Yesterday I uploaded a Bioclipse feature that adds a rdf manager to handle RDF content, which includes SPARQL support. The below snippet shows application to the solubility data [3]:

Maybe RDF support in Eclipse is an idea for its Google Summer of Code?

See also:

1. One Billion Biochemical RDF Triples!
2. RDF-ing molecular space
3. Solubility Data in Bioclipse #1