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): 1 minute read

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. And, I have set up a new JChemPaint trunk/ where I have moved Niels’ demo editor. 1 minute read

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: 1 minute read

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. 1 minute read

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. less than 1 minute read

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. The BibTeX mapping examples are under discussion, but provide some insight to those who are used to using that (JabRef users, for example). 3 minute read

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. 4 minute read