• Jan 12, 2011

    Karolinska Institutet

    Hi all, and a happy 2011! After a turbulent December (finishing up in the Oscar project), holidays, etc, I am starting to get some sense of organization in my new position at the Institutet för miljömedicin at the Karolinska Institutet in Stockholm. I will be using cheminformatics and chemometrics methods in toxicology studies, and work in the groups of Prof. Roland Grafström and Prof. Bengt Fadeel. less than 1 minute read
  • Dec 30, 2010

    The 100th Blue Obelisk 2006 paper citation

    Two and a half months after the CDK milestone, the Blue Obelisk paper also reached 100 citations. Here the lucky paper is Design, Synthesis, and Preclinical Evaluation of New 5,6- (or 6,7-) Disubstituted-2-(fluorophenyl)quinolin-4-one Derivatives as Potent Antitumor Agents by Chou et al (doi:10.1021/jm100780c). The Blue Obelisk paper (doi:10.1021/ci050400b) is cited because the authors used OpenBabel. About half of the 100 citations is because OpenBabel was used, whereas OpenBabel is only mentioned as one of the Blue Obelisk-associated unprojects in the Blue Obelisk paper. less than 1 minute read
  • Dec 30, 2010

    Text mining chemistry from Dutch or Swedish texts

    Oscar is a text miner. It mines in text for chemistry. Oscar4 is the next iteration of Oscar code that I worked on in the past three months, with Lezan, Sam, and David. I blogged about aspects of Oscar4 at several occasions: 3 minute read
  • Dec 30, 2010

    Blogging as part of your workflow

    Today is the last day I work on Oscar in my position in Cambridge (tomorrow I have a day off and fly back to Sweden). Three months go quick indeed. Next Monday I start my position in Stockholm at the IMM department at the Karolinska Institutet on predictive toxicology. Back in Sweden, it is. Well, of course, I worked from home most of the time anyway. 1 minute read
  • Dec 29, 2010

    Converting JSON to RDF/XML with Groovy

    Mark’s new CCO/RDF hosting functionality (see also my post two days ago ) requires RDF/XML format, so I updated my code to convert the Chempedia Substances data into RDF/XML instead of N3 (I have asked Rich to put a new download link online). This is the Groovy code I used: less than 1 minute read
  • Dec 27, 2010
  • Dec 27, 2010