Activity of Antioxidants Against Cancer Target(s)

Using the OpenPHACTS database and d3.js data visualization library

by Taís Ribeiro & Tim van de Goor

Research Question

What is the activity of antioxidants (present in the OpenPHACTS database) against different free radicals (e.g. a carcinogenic radical)?

Problems and Challenges

1. Finding the right target molecule (free radical)

2. Filtering the JSON results from OpenPHACTS API call

3. Unifying activity units (%, M, g/L)

4. Linking antioxidants to food sources

5. Other visualization techniques from d3.js library

Finding the right target molecule

Most common in OpenPHACTS results:

- DPPH (a standard probing radical)

- ABTS (a standard probing radical)

- Nitric Oxide

- Peroxide

- Superoxide

Filtering the JSON results

- Hardcoded exceptions:

Unifying activity units

- Selected %, uM and ug/mL as standard units

- Conversion by hardcoded exceptions:

(Other) visualization techniques

- Simple d3.js scatterplot

- Scaling x-axis, category y-axis

- Used jquery.tipsy.js for tooltips on mouseOver

- Visual effects for datapoints using d3.js- Description below shown onClick

- Optional HTML table with results

Code execution

conceptSearcher.byTag()

compoundSearcher.compoundPharmacologyCount()

compoundSearcher.compoundPharmacology()

conceptURI conceptURI

# of results

JSON.stringify(response)

responsehasAssay.description

publishedUnits

publishedValueUnit conversion

Radicalfilter

d3.js scattergraph

description

(x,y)

color

jquery.tipsy.js

onClick()

visualization

processing

request

input

HTML table

search box and buttonfree radical target selectionactivity unit selection

d3.js scatter plot

jquery.tipsy.js tips on mouseOver

data points with opacity

units and scale change

visualization options

table with results

description onClick

Summary

What’s working:

- search (term to conceptURI,

- results processing (units, values)

- visualization (d3.js, tipsy.js)

- diagnostics (JSON replies, no. of (filtered) results, conceptURI)

What’s not working:

- Search suggestions

- Error handling (partially)

Difficulties:

- Graph and axes layout

- Server problems, changes in JSON formatting

Outlook

- Combining results with food database

- Motivation for unification of units across OpenPHACTS database

Demo