chem-bla-ics: April 2015

"Open Data in Science"

Recently, I got invited to a meeting of Eindhoven's Social Media Club, which has interesting meetings in the knowledge city capital of The Netherlands [ref]. This months topic was Open Data and I was asked to present Open Data in research, which I eagerly accepted. The quite liked the title too: The great wide Open Data.

I very much enjoyed the other presentation too, mostly by Allard Couwenberg, whom gave an excellent introduction into Open Data, which simplified my presentation, allowing me to focus on the role of Open Data in research and possible at universities. For example, I discussed that I think we can improve the quality of our education of we improve the access to knowledge for our students.

Apr

Bioclipse 2.6.2 with recent hacks #1: Wikidata & Linked Data Fragments

Us chem- and bioinformaticians have it easy when it comes to Open Science. Sure, writing documentation, doing unit testing, etc, takes a lot of time, but testing some new idea is done easily. Yes, people got used to that, so trying to explain that doing it properly actually takes long (documentation, unit testing) can be rather hard.

Important for this is a platform that allows you to easy experiment. For many biologists this environment is R or Python.

Apr

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.

Apr

CC-BY with the ACS Author Choice: CDK and Blue Obelisk papers liberated

Already a while ago, the American Chemical Society (ACS) decided to allow the Creative Commons Attribution license (version 4.0) to be used on their papers, via their Author Choice program. ACS members pay $1500, which is low for a traditional publisher.

Apr

Ambit.js 0.0.2 release: a scatterplot

Two weeks ago I made a second release of ambit.js, a small project to show the power of the eNanoMapper API (doi:10.5281/zenodo.16517). It still is a client library to use the API from JavaScript and a few weeks ago I posted a few screenshots.

Apr

Getting CAS registry numbers out of WikiData

doi 10.15200/winn.142867.72538

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:

PREFIX wd: <http://www.wikidata.org/entity/>

SELECT ?compound ?id WHERE {

?compound wd:P231s [ wd:P231v ?id ] .