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Sunday, January 11, 2015

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.

ACE inhibitors
The first team (Mischa-Alexander and Hamza) focused on the ACE inhibitors (type:"drug class") and the WP554 from WikiPathways. The use a tree structure to list inhibitors along with their activity:


The source code for this project is available under a MIT license.

Diabetes
The second team (Catherine and Moritz) looked at compounds hitting diabetes mellitus targets. They take advantage from the new disease API methods and first ask for all targets for the disease, and then query for all compounds. Mind you, the compounds are not filtered by activity, so it mostly shows interactions that real targets.


This product too is available with the MIT license.

Tuberculosis
The third project (Nadia en Loic) also goes from disease to targets and they looked at tuberculosis.

Asynchronous calls
If you know the ops.js, d3.js, and JavaScript a bit, you know that these projects are not trivial. The remote web service calls are made in an asynchronous manner: each call comes with a callback function that gets called when the server returns an answer, at some future point in time. Therefore, if you want to visualization, for example, compounds with activities against targets for a particular disease, you need two web service calls, with the second made in the callback function of the first call. Now, try to globally collect the data from that with JavaScript and HTML, and make sure to call the visualization call when all information is collected! But even without that, the students need to convert the returned web service answer into a format that d3.js can handle. In short: quite a challenge for six practical days!

Friday, January 09, 2015

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

The Royal Society of Chemistry and Wikipedia just released an interesting press release:
    "The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and databases – to be used by Wikipedia editors who write about chemistry. The partnership is part of a wider collaboration between the Society’s members and staff, Wikimedia UK and the Wikimedia community. The collaboration is working to improve the coverage of chemistry-related topics on Wikipedia and its sister projects."
This leaves me with a lot of questions. I asked these in a comment awaiting moderation:
    Can you elaborate on the conditions? Is it limited to wikipedia.org or does it extend to other Wikimedia projects, like Wikidata? Does the agreement allow manual lookup of information only, or does it allow text mining on the literature as well as on the database? How should I put this in perspective with the UK law that allows text mining, and, in particular, can UK Wikipedia editors use text mining anyway, or is that restricted? Is there an overview of the details of what is allowed and not allowed, or a list of restrictions otherwise?
Details on how to apply to access can be found here.