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

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:

2 minute read

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.

1 minute read

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):

1 minute read

TODO: April 2nd, defend my PhD work

In 4.5 weeks, on Wednesday April 2 (13:30 precisely, Aula, Comeniuslaan 2, Nijmegen) I will publicly defend my PhD work performed in the Analytical Chemistry group of Prof. Lutgarde Buydens at the Radboud University Nijmegen:

6 minute read

Where's the maize genome torrent?!?

/. just posted a story about the maize genome just published, for which the sequences can be downloaded from this FTP site. The files are not that large at all. But it makes me wonder… where are the .torrent files for the sequenced genomes? Here’s Davids catch on the story.

less than 1 minute read