RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points. The MyExperiment team has set up an excellent RDF front end. For example, this is my MyExperiment account in RDF. The storage gets updated once every day (at this moment), but I’m sure that will become more often in the future.

Nature Chemistry just released the first issue with a few free papers, like Asymmetric total syntheses of (+)- and (-)-versicolamide B and biosynthetic implications by Miller et al. (DOI:10.1038/nchem.110). Now, we’ve seen the Royal Society of Chemistry’s Project Prospect (see RSC: the first publisher to go semantic!) and ChemSpiders recent ChemMantis system which enriches the papers with machine readable representations of the

There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.

Two companies recently showed two things: open access and open data allow adding value adding value is easier by forking Rich’ MetaMolecular set up Chempedia which combines a substructure-searchable chemical Wikipedia. There is also a page to make links to new Wikipedia monographs.

Fourth in the CDK Literature series. Really, a follow up on #3 which I wanted to get out, even though not really finished yet. But, after 3 comes 4, not 3b. Maybe 3.1, but that suggests at least 3.2-3.9 too, let alone full R (that was supposed to the space of all reals…) I’ll stick to positive non-zero integers. #1 and #2 are still available too.

Ola blogged about something he is working on for Bioclipse2. The next major series of Bioclipse releases will use the RCP-based resource architecture, which allows better integrating with other RCP plugins, such as the Subclipse plugin which allows one to browse Subversion repositories directly in Bioclipse. That is cool! Check out the screenshot he posted in his blog. Now, this kind of integration is important.

The results for the Open Lab 2007 are out . I participated in this endeavor as judge, and read 75 of the 486 blog items, focusing on the sections chemistry, blogging, publishing, politics of science , and a number of blog items with few reviews when I passed them. I am happy to see that one of the chemistry submission I made myself made it into the anthology: the Depth-First item on SMILES and Aromaticity: Broken?

Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, discussing and comparing different offerings like Pipeline Pilot, Taverna, and KNIME.

Pending the release of Bioclipse 1.2.0, Ola asked me to do some additional feature implementation for the QSAR feature, such as having the filenames as labels in the descriptor matrix.

The Chemistry Development Kit has never really been without any bugs, which is reflected in the number of failing JUnit tests.

The OD part of ODOSOS is getting more and more attention, and it seems that Peter’s Open Data battle is paying off (see his original OpenData article in Wikipedia): an open data specific license has reached the beta stage (see this announcement). The idea behind this licenses seems to come down to: I am looking forward how this license will be picked up by the community. PubChem may be a good candidate to use this license;