chem-bla-ics: May 2015

Bioclipse 2.6.2 with recent hacks #3: using functionality from the OWLAPI

Update: if you had problems installing this feature, please try again. Two annoying issues have been fixed now.

Third in this series is this post about the Bioclipse plugin I wrote for the OWLAPI library. This manager I wrote to learn how the OWLAPI is working. The OWLAPI feature is available from the same update site as the Linked Data Fragments, so you can just follow the steps outlined here (if you had not already).

Using the manager

The manager has various methods, for example, for loading an OWL ontology:

ontology = owlapi.load(

"/eNanoMapper/enanomapper.owl", null

);

If your ontology imports other ontologies, you may need to tell the OWLAPI first where to find those, by defining mappings.

May

New: DOI hyperlinks in the CDK JavaDoc

Apparently I never extended the cdk.cite JavaDoc Taglet to use DOIs from the bibliographic database to create hyperlinks in the JavaDoc. But fear no more! I have submitted a simple patch today to add these to the JavaDoc, and I assume it will be part of the next CDK release from the master branch.

Of course, many papers in this bibliographic database (i.e.

May

Re: "Thank you for sharing"

Nature wrote a piece on data sharing (doi:10.1038/520585a). It remains a tricky area to write about, particularly those terms like public access. Researchers are still a bit shy in sharing data, in some fields more than in others. And for valid reasons. Data sharing is a choice, it is something you do to get something in return. The return you get on your investment can vary, for example:

goodwill (e.g.

May

Bioclipse 2.6.2 with recent hacks #2: reading content from online Google Spreadsheets

Update 2015-06-04: the authentication with the Google Drive has changed; I need to update the code and am afraid I missed the point, so that the below code is not working right now :(

Similar to the previous post in this new series, this post will outline how to make use of the Google Spreadsheet functionality in Bioclipse 2.6.2.

May

CDK Literature #6

Originally a series I started in the CDK News, later for some issues part of this blog, and then for some time on Google+, CDK Literature is now returning to my blog. BTW, I created a poll about whether CDK News should be picked up again. The reason why we stopped was that we were not getting enough submissions anymore.

For those who are not familiar with the CDK Literature series, the posts discuss recent literature that cites one of the two CDK papers (the first one is now Open Access).

May

Groovy Cheminformatics with the CDK - 11th edition

It's been a while since I blogged about a release of my "Groovy Cheminformatics with the CDK" book, but not too long ago I made another release, 1.5.10-0. This was also the first one with white paper, and updated for the latest CDK development release.

There are two versions (and always check the special deals, e.g.

May

Pathways as summaries: Nature Review Disease Primers and Open Source Malaria

Event 1

The Nature Publishing Group (NPG) has launched a new journal, which you probably did not miss. There is founding editorial titles From mechanisms to management (doi:10.1038/nrdp.2015.1) as the goal of the journal. Very noble and very needed, indeed! They write:

Each Primer article includes the same major sections: epidemiology, mechanisms, pathophysiology, diagnosis, screening, prevention, management and patient quality of life.