Coding an OWL ontology in HTML5 and RDFa

There are many fancy tools to edit ontologies. I like simple editors, like nano. And like any hacker, I can hack OWL ontologies in nano. The hacking implies OWL was never meant to be hacked on a simple text editor; I am not sure that is really true. Anyways, HTML5 and RDFa will do fine, and here is a brief write up. This post will not cover the basics of RDFa and does assume you already know how triples work. If not, read this RDFa primer first. 3 minute read

PubChemRDF: semantic web access to PubChem data

Gang Fu and Evan Bolton have blogged about it previously, but their PubChemRDF paper is out now (doi:10.1186/s13321-015-0084-4). It very likely defines the largest collection of RDF triples using the CHEMINF ontology and I congratulate the authors with a increasingly powerful PubChem database. less than 1 minute read

Chemistry Central and the ORCID identifier

If you are a scientist you have heard about the ORCID identifier by now. If not, you have been focusing on groundbreaking research and isolated yourself from the rest of the world, just to make it perfect and get that Nobel prize next year. If you have been working on impactful research, Nobel prize-worthy, and have been blogging and tweeting about your progress, as a good Open Scholar, you know ORCID is the DOI for “research contributors” and you already have one yourself, and probably also that T-shirt with your own identifier. Mine is 0000-0001-7542-0286, and almost 1.3M other authors got one too. The list of ORCIDs on Wikipedia is growing (and Wikidata), thanks to Andy Mabbett, whom also made it possible to add your ORCID on WikiPathways. 1 minute read

Getting CAS registry numbers out of WikiData

I have promised my Twitter followers the SPARQL query you have all been waiting for. Sadly, you had to wait for it for more than two months. I’m sorry about that. But, here it is: 1 minute read

Programming in the Life Sciences #21: 2014 Screenshots #1

December saw the end of this year’s PRA3006 course (aka #mcspils). Time to blog some screenshots of the student projects. Like last year, the aim is to use the Open PHACTS API to collect data with ops.js and which should then be visualized in a HTML page, preferably with d3.js. This year, all projects reached that goal. 1 minute read

"Royal Society of Chemistry grants journals access to Wikipedia Editors"

The Royal Society of Chemistry and Wikipedia just released an interesting press release: 1 minute read

Programming in the Life Sciences #20: extracting data from JSON

I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies, but perhaps JSON-LD combines the best of both worlds. 2 minute read