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.
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.
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.
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.
Bioinformatics just published a paper from Schuemie and Kors (Erasmus University/NL, BioSemantics group): Jane: suggesting journals, finding experts (doi:10.1093/bioinformatics/btn006):
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.
/. 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.
Some days have passed , and the Debian mirrors have now picked up the CDK package (unstable only so far), allowing you to sudo aptitude install libcdk-java from your favorite local mirror. The details are available from this packages.debian.org/libcdk-java page. The fact that it is listed as contrib is a small mistake; the package is really main material.
Michael Koch (aka man-di) and Daniel Leidert (as part of the pkg-java team) have worked on packaging the CDK. The ran into some issues, such as the CDK build system not perfectly compatible with the Debian java libraries in /usr/share/java. Both detection of the available libraries as well as putting them in the classpath, caused trouble with the CDBS-based build system wrapping around the Ant build.xml (note the many commit this weekend ;).
Jim replied to the request by Anthony in my blog for a bug track system for CrystalEye (in beta), after a discussion on the CIF processing pipeline (see [here] (https://chem-bla-ics.linkedchemistry.info/2008/01/30/why-chemistry-rich-rss-feeds-matter.html), here, here and here).
Mathieu Fourment (et al.) just published a paper on some performance testing on 6 programming languages in BMC Bioinformatics: A comparison of common programming languages used in bioinformatics (doi:10.1186/1471-2105-9-82). The below figure is from the paper, for a sequence alignment exercise (copyright with paper authors, OpenAccess license of journal):