Visualizing Scaffold Trends

Recently Barbara Zdrazil and I published an article that explored the idea of tracking the attention being paid to a scaffold in the medicinal chemistry literature (as represented by ChEMBL). The gist of the idea is that scaffolds that are more frequently enumerated or tested in more assays (or even published in increasingly high IF […]

Waterfall Plots for Dose Response Curves

Waterfall plots are a common visualization method to view multiple spectra and have some similarities with joy plots. In the high throughput screening world, people have plot multiple dose response curves, offset on the z-axis to produce something that looks like a waterfall. An example is Figure 1 in Inglese et al, PNAS, 2006, 103(31). […]

Exploring ChEMBL Targets with Neo4j

As part of an internal project I’ve recently started working with Neo4j for representing and querying relationships between entities (targets, compounds, etc.). What has really caught my attention is the Cypher graph query language – by allowing you to construct queries using graph notation, many tasks that would be complex or tedious in a traditonal […]

Summarizing Collections of Curves

I was browsing live notes from the recent IEEE conference on visualization and came across a paper about functional boxplots. The idea is an extension of the boxplot visualization (shown alongside), to a set of functions. Intuitively, one can think of a functional box plot as specific envelopes for a set of functions. The construction […]

Exploring co-morbidities in medical case studies

A previous post described a first look at the data available in, 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 […]