ChEMBL-RDF: Uploading data to Kasabi with pytassium

I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi. less than 1 minute read

Bioclipse-Oscar4 - Text mining in Bioclipse

Almost a year ago I started a position with Peter Murray-Rust to work on Oscar for three months (see this overview of results; a paper by the full Oscar team (Sam, David, Dan, Lezan) is pending, and I’m really happy to have been able to contribute bits to the project). Since then, I have had little time :( That’s how it goes, with post-hopping, unfortunately. One thing I did do after that, was write a Bioclipse plugin. 1 minute read

InChIKey collision: the DIY copy/pastables

About two weeks ago, the ChemConnector blog reported an InChIKey collosion detected by Prof. Goodman . Unlike the previous collision, this one was based solely on the graph and not on stereochemistry. The two molecules both have the InChIKey OCPAUTFLLNMYSX-UHFFFAOYSA-N: less than 1 minute read

My Google Scholar Citations profile arrived

Web of Science is my de facto standard for citation statistics (I need these for VR grant applications), and defines the lower limit of citations (it is pretty clean, but I do have to ping them now and then to fix something). The public front-end of it is Researcher ID. There is an Microsoft initiative, which looks clean but doesn’t work on Linux for the nicer things, but the coverage of journals is pretty bad in my field, giving a biased (downwards) H-index. And CiteULike and Mendeley focus more on your publications than on citations (though the former has great CiTO support!). 1 minute read

Groovy Cheminformatics 3rd edition

Update: the fourth edition is out. less than 1 minute read

Data, Nonotify, or Silent?

I cannot find the bug report just now, but the CDK has an open problem with change even notification, where the nonotify classes still caused change event to be sent around. 2 minute read

ChemPedia-RDF #2: Kasabi

Kasabi is a new, RDF hosting service by Talis. It’s still in beta, and I have been testing their beta service with the RDF version I created of ChemPedia Substances (the now no longer existing cool web service from MetaMolecular to draw and name organic molecules). 2 minute read