"Emerging practices for mapping and linking life sciences data using RDF"

The “Emerging practices for mapping and linking life sciences data using RDF” (doi:10.1016/j.websem.2012.02.003) is now available online, where I contributed a section on the original workflow for creating ChEMBL triples, and contributed to the section about open licensing, referring to CCZero and the Panton Principles. Happy reading! less than 1 minute read

ChEMBL 13 as RDF

Update: this work is now described in this paper . less than 1 minute read

CiTO / CiteULike: publishing innovation

Readers of my blog know I have been using the Citation Typing Ontology, CiTO (doi:10.1186/2041-1480-1-S1-S6). I allows me to see how the CDK is cited and used . CiteULike is currently adding more CiTO more functionality, which they started doing almost one and a half years ago. 1 minute read

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

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

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