chem-bla-ics: March 2008

CDK Module dependencies #2

A bit over 2 years ago I published a UML diagram showing the dependencies between CDK modules. Since then I lot of new modules have been defined, added or factored out from the extra module (click to zoom):These kind of diagrams help us maintain the library, and apply some design goals, as explained in the first post on this.

If one compares the two diagrams, one sees that fewer code depends on the data module, but it is also clear that still a lot of them do. Another issue that had not properly addressed yet, is that a lot of modules still depend on the extra module, which aggregates everything that had not been assigned elsewhere.

Parallelism

This diagram also helped me use the Ant <parallel> task to allow compiling CDK modules in parallel, instead of sequentially.

Mar

Be in my Advisory Board #3: JChemPaint widgets?

As promised, I am working on JChemPaint. I have progressed in cleaning up the CDK trunk/ repository by removing traces of the old JChemPaint applet and application. And, importantly, removed the GeometryTools class that took rendering coordinates. The history here is that the original GeometryTools was renamed to GeometryToolsInternalCoordinates, but is now available as

GeometryTools again. I still have to merge Niels' additions with it, though.

Mar

My FOAF network #5: SPARQL-ing my network

FOAF rulez: it's RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame. I have to catch the train in about 15 minutes, so will not elaborate too much, but here are some Sesame 2.0.1 work:> create native.

Mar

My FOAF network #4: Tabulating my publications

Richard informed me (via Planet RDF) about N3 support in Tabulator. N3 is a more compressed version of RDF/XML, which I have been using so far, but both are RDF. Now, I don't plan to use N3 for my FOAF experimenting, but two things caught my eye in the nice blog item.

First, it has a very useful tip on .htaccess which you can use to teach Apache about MIME types, even when you do not have root access.

Mar

Sugammadex: the molecular condom

Two things I like blogging: 1. the turn-over of information; 2. the informal nature. There are more. The turn-over is optimized by commonly: 1. short blog items; 2. easily allows scanning tons of headlines; 3. often full of links if you want to know the details.

Today, my eye was caught by Sugammadex Buzz for Organon over at Lamentations on Chemistry. The reason was Organon, which is just around the corner here. They had news about a new drug.

Mar

My FOAF network #3: My publications

As promised, I'll write a bit about using Bibliographic Ontology Specification (BIBO) over as bibliontology.com. I have written a basic XSLT to create a HTML GUI (open the RDF source in e.g. Firefox). Really basic: it only converts articles, and even assumes some conventions I found in examples in the BIBO wiki. I have not spotted a BIBO validator yet, so guessing a bit.

Mar

The Chemical Object Identifier; or, the freedom to identify chemicals

IUPAC chemical names, SMILES and InChIs are too long. InChIKeys are not unique enough because of safety reasons (you have a 1 in 10 billion chance of blowing up your building; well, odds are actually much, much lower than getting hit by Osama or friends, let alone a car). Wikipedia URIs do not cover enough chemical space.

However, we need short identifier. Why, actually? Computers don't care about long identifiers. Systems can be integrated. A web link is easy to make. But we do.

Mar

My FOAF network #2: XSLT for a HTML GUI

Because the ACS meeting where Henry will present something about FOAF in chemistry, is nearing very fast now (here's the first blog it this series), it becomes urgent to beef up the Blue Obelisk FOAF network, now consisting of 7 members. All do now show up in the FOAFExplorer:

Now, to make sure that my FOAF is in order, I set up the regular XML/RDF toolchain, using xmllint to validate the XML and RDF syntax, and XSLT to convert the FOAF to human readable HTML.

Mar

Metabolomics Ontologies: SKOS-ified the ArMet specification

The MetWare project is going to make use of ontology technologies to control the content of the database, and a first step is to convert our MetWare database design into something using a formal ontology language. I have played with OWL in the past (see for example its use in Bioclipse), but was not overly happy with it in all situations.

Then I read about SKOS, Simplified Knowledge Organisation System. Unlike OWL, SKOS is less strict on relations between concepts being marked up.

Mar

Jane, find me interesting journals, please.

Bioinformatics just published a paper from Schuemie and Kors (Erasmus University/NL, BioSemantics group): Jane: suggesting journals, finding experts (doi:10.1093/bioinformatics/btn006):Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g.