Exploring co-morbidities in medical case studies

A previous post described a first look at the data available in casesdatabase.com, primarily looking at summaries of high level meta-data. In this post I start looking at the cases themselves. As I noted previously, BMC has performed some form of biomedical entity recognition on the abstracts (?) of the case studies, resulting in a set […]

Exploring medical case studies

I recently came across http://www.casesdatabase.com/ from BMC, a collection of more than 29,000 peer-reviewed case studies collected from a variety of journals. I’ve been increasingly interested in the possibilities of mining clinical data (inspired by impressive work from Atul Butte, Nigam Shah and others), so this seemed like a great resource to explore The folks […]

Updated version of rcdk (3.2.3)

I’ve pushed updates to the rcdklibs and rcdk packages that support cheminformatics in R using the CDK. The new versions employ the latest CDK master, which as Egon pointed out  has significantly fewer bugs, and thanks to Jon, improved performance. New additions to the package include support for the LINGO and Signature fingerprinters (you’ll need the […]

Support for feature,count fingerprints in fingerprint 3.5.0

I’ve just updated the fingerprint package to v3.5.0 (should show up on CRAN shortly, or else you can get it directly from my Github repository). The main update in this version is better support for feature,count type fingerprints. An example would be ECFP or signature fingerprints. In these types of fingerprints, the output is usually […]