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 […]

Words, Sentences, Fragments & Molecules

For some time I have been thinking of the analogy between linguistics (and text mining of language data) and chemistry, specifically from the point of view of fragments (though, the relationship between the two fields is actually quite long and deep, since many techniques from IR have been employed in cheminformatics). For example, atoms and […]

Annotating Bioassays

I’ve been working for some time with the PubChem Bioassay collection – a set of 1293 assays that cover a range of techniques (enzymatic, phenotypic etc.), targets and sizes (from 20 molecules to 200,000 molecules). In addition, some assays are primary, high-throughput assays whereas a number of them are smaller, confirmatory assays. While an extremely […]