chem-bla-ics: September 2010

Visualizing data embedded in XHTML+RDFa

Orion picked up my challenge and made an web based application to graph data from one of my XHTML-RDFa pages. Well done! He wrote his work up in his blog of which the results looks like:

The text field shows the SPARQL used to aggregate the data, which is then visualized in the plot below that field. You can edit the SPARQL and, for example, plot the boiling point (t) as function of the number of carbons (p):

This work nicely shows some interesting McPrinciples: it shows what happens if we allow reuse and share our knowledge; it shows that nice graphics and semantic access to original data are very compatible.

Sep

Quo vadis, CDK?

Tomorrow it is 10 years ago that the CDK was founded. The project has considerably grown and has a high impact on science. The CDK code base did not start 10 years ago, but was founded on the code bases of CompChem, JChemPaint, and Jmol, but has seen several reincarnations since the start.

Sep

Using PubChem to create CDK unit tests

In 2008 I posted about Wicked chemistry and unit testing and was using BeanShell at the time to convert a structure on PubChem into CDK source code. But since I rather use Groovy now, I have updated the code. I used CDK 1.3.6 and the PubChem XML format now.:

import org.openscience.cdk.Molecule; import org.openscience.cdk.io.*; if (args.length == 0 || args[0] == null) { System.out.println("Syntax: pc2ut.groovy [CID]\n"); System.exit(0); } String cid = args[0]; String urlString = "http://pubchem.

Sep

Presentation at AstraZeneca

Today and tomorrow I am guest at AstraZeneca in Mölndal. This is the presentation I gave today about the work on Bioclipse-RDF:

The Semantic Web for Life SciencesView more presentations from egonw.

Sep

Noel's chemical ASCII art

Very short post, but this is brilliant! Not sure if Noel posted this in reply to this Blue Obelisk eXchange question, but certainly answers it:

Noel, very nice post!

Sep

The CDK 2003 paper is now cited 99 times

The 100th paper, or the first one that is not mine, I will give a

special review in my blog.

Sep

A list of things I miss in CiteULike

AJCann posted a blog today about what he doesn't like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).

Agreeing with @citeulike and @abhishektiwari, as a service provider any bad news is good news too: they provide opportunities to improve.

Sep

xournal: free annotator for PDFs

See http://xournal.sourceforge.net/ or go for 'sudo aptitude install xournal'.

Sep

Call for Papers: Thematic Series about RDF in Chemistry

As a follow up of the ACS RDF 2010 Symposium we just had in Boston, I can announce that we are preparing a thematic series in the Journal of Cheminformatics around this theme, and that at least six speakers will present their work in this series.

Sep

CDK 1.3.6: the changes, authors, and reviewers

The list of changes is particularly long for this development release. Therefore, I will list the authors and reviewers first. Note that this release also includes the changes of the 1.2.6 and CDK 1.2.7 release.

The authors

I am mildly impressed by this release's list of authors... it is certainly not the usual suspects anymore, and I would like to thank all contributors very much.