RDF in Chemical blogspace

I have been playing with RDF-ing molecular space a bit, and results are getting slowly in shape:



This screenshot shows the HTML created for this RDF file on the fly by the web browser. The current version extracts information from Chemical blogspace and ChEBI (not much yet, though :).

The molecule pages in Chemical blogspace link to this RDF, and that's really what I wanted to show right now:



Why I do this? Among others, give me all boiling points for some compound with one (SPARQL) query, instead of having to browse several web resources manually. Oh, BTW, the HTML view of the RDF document uses chemical RDFa.

Userscripts you forget about...

Peter writes about a Greasemonky userscript pop up:

What are the Pg and Cb all over the TOC. When you bring up the page they aren’t there! What’s happened? Well the chemical blogosphere has posted about several articles here and mentioned their DOIs. The Blue Obelisk has developed a Gresemonkey script (which is a Firefox plugin) which reads the TOC and sees if any DOIs have been mentioned in the Chemical Blogosphere. And, in this case, three articles have been.

This is the screenshot he made:

For the obligatory statistics: Cb now discusses 1184 articles. Because I have trouble accessing the Postgenomic website, I cannot give that number :(

The rise of Chemical blogspace

The Chem Blog wrote about WTF is up with the Science blogosphere?, discussing a podcast on the chemical blogosphere, and wondering why it is larger than that of other natural science fields and mathematics. It is surprising indeed, because chemists generally are very conservative when it comes to anything to do with a monitor, mouse and keyboard. The argument put forward in the podcast is that there are a few strong voices amongst our blogs.

I am hoping the Chemical blogspace helps a bit too here. With about 40 unique users a day it is somewhat lower than it has been before the move to the new server, which was around 60 visitors each day, but I am sure this will recover.

The number of chemistry related blogs is rather large indeed, and the Cb counter is at over 136 now. Not every blog is equally active, but both the absolute number of entries and the number of active blogs per week are continuously increasing:


Interestingly, the blog had a very nice plot of the blogosphere interconnectivity. It is good practice to link to many other blogs and resources in ones entries, to keep discussions going, provide further information etc. Like Peter I was hoping that the plot would refer the Chemical blogspace, but it does not. This interconnectivity information is available from the Cb database, and I will try to create such a plot.

RDFa Operator in action on Cb

I reported yesterday on my efforts (and Mike's help) to get RDFa for chemistry going. I did not have time to add the new HTML code to Cb, but have done so now:

Read my Chem-bla-ics blog for the details.

More molecules in Cb

Because the use of chemical microformats and RDFa is not yet picking up, I extended Cb to detect molecules via Wikipedia. This is paying off, even though a lot of Wikipedia entries do not list InChIs: the list is much longer now, and covers a much larger set of blogs. Thanx to all who link to Wikipedia when naming a chemical compound!

New Blogs #7

These are the new blogs that entered Chemical blogspace in the last month:

• The Bioenergy Blog (entry in Cb)
• Ryan's Blog on NMR Software (entry in Cb)
• Totally Retrosynthetic (entry in Cb)
• Marcus D. Hanwell's Blog (entry in Cb)
• LaserJock » Chemistry (entry in Cb)
• Sciurus' Blog (entry in Cb)
• DaLe's private Blog (entry in Cb)
• Jerome's Blog Space (entry in Cb)
• Chemical & Process Engineering (entry in Cb)
• Eye on DNA (entry in Cb)
• Pharmacophores in Jmol project (entry in Cb)
• docking.org Story Search (entry in Cb)

Suggestions are most welcome, and thanx to those who did in the last month.

Cb moved to new location...

Because the CUBIC has shutdown, and my desktop machine there will be removed shortly, I moved the Chemical blogspace homepage to:

  http://cb.openmolecules.net/

This is replacing the temporary hosting at SourceForge. The webpage is now hosted by the Geoff of OpenBabel.

Userscripts
If you run one of the script which adds comments from Cb to either DOIs or InChIs, you need to adapt the script you have installed and replace in all URLs wiki.cubic.uni-koeln.de/pg/ or wiki.cubic.uni-koeln.de/cb/ with cb.openmolecules.net/.