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 QuestionWhat is the activity of antioxidants (present in the OpenPHACTS database) against different free radicals (e.g. a carcinogenic radical)?
Problems and Challenges1. Finding the right target molecule (free
radical) 2. Filtering the JSON results from
OpenPHACTS API call3. Unifying activity units (%, M, g/L) 4. Linking antioxidants to food sources5. Other visualization techniques from d3.js
library
Finding the right target moleculeMost 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 executionconceptSearcher.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 resultsdescription onClick
SummaryWhat’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