I noted earlier this week that [d]uring the week [in Oxford ], someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow;
The meetings in and around Oxford were great! I already wrote that the Predictive Toxicology workshop was brilliant (see Oxford… #1 ) and Oxford… #2 ), but I also very, very much enjoyed meeting up with Dan and Nico! During the week, someone (name and address is know at the editorial office) commented on the fact that my blog posts are somewhat difficult to follow; that is, it’s often not clear why I am posting what I am posting.
The Predictive Toxicology meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data.
Yesterday I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites , but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges.
The announcement of the Panton Principles is the big news today, though Peter already spoke about them in May last year (see coverage on FriendFeed and Twitter). The four principles list in their short versions: When publishing data make an explicit and robust statement of your wishes. Use a recognized waiver or license that is appropriate for data.
Well, you might spot a pattern here; yes, another chemical SPARQL end point (actually, it shares the end point with the Solubility data). This time around Rich’s ChemPedia. Taking advantage of the CC0-licensed downloads , I have created a small Groovy script (using this JSON library) to convert the ChemPedia JSON into Notation3: import net.sf.json.groovy.JsonSlurper;
With pleasure I read Analogue or Digital? - Both, Please. Funnily, I just created MP3 (or, preferably Ogg Vorbis, superior but hardly any support by commercial companies, who rather seem to pay license fees) directly from the CD. Anyway… the blog wanders of to Google introducing searchable books, with many out-of-copyright.
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.