Dereferencable InChIs: OpenMolecules RDF

About four and a half years ago, I started OpenMolecules RDF, a spin off from Chemical blogspace (Cb, which is still up and running thanks to Peter Maas!) where I started using InChIs in URIs . My interest came from the dereferencability, the ability to take an InChI and find information about the chemical structure representated by it. Because information about anything is scattered around the internet, and we need something decentralized. Moreover, at the time searching of InChIs with search engines like Google did not work well at all: InChIs were tokenized in inconvenient ways. 1 minute read

"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

Visualizing metabolite fluxes on WikiPathways pathways using a PathVisio plugin

Visualizing metabolite fluxes on WikiPathways pathways using a PathVisio plugin 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

Groovy Cheminformatics 4th edition

Six month was not quite the amount of time I anticipated between the third and fourth edition, but I finally managed to upload edition 1.4.7-0 of my Groovy Cheminformatics book. The first three editions sold 37 copies, including two for myself. Enough to feel supported and to continue working on it. 2 minute read

Oscar4 paper: text mining in Bioclipse (and everywhere else, of course)

The Oscar4 paper (CC-BY, just like the screenshots of the paper below) was out already some days now, but the formatting has finished: less than 1 minute read