1. Activity of Antioxidants Against Cancer Target(s)
Using the OpenPHACTS database and d3.js data visualization library
by Taís Ribeiro & Tim van de Goor

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

3. Problems and Challenges
Finding the right target molecule (free radical)
Filtering the JSON results from OpenPHACTS API call
Unifying activity units (%, M, g/L)
Linking antioxidants to food sources
Other visualization techniques from d3.js library

4. Finding the right target molecule
Most common in OpenPHACTS results:
- DPPH (a standard probing radical)
- ABTS (a standard probing radical)
- Nitric Oxide
- Peroxide
- Superoxide

5. Filtering the JSON results
- Hardcoded exceptions:

6. Unifying activity units
- Selected %, uM and ug/mL as standard units
- Conversion by hardcoded exceptions:

7. (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

8. Code execution request visualization processing
compoundSearcher.compound
Pharmacology
Count()
conceptURI
conceptURI
input
compoundSearcher.compound
Pharmacology()
conceptSearcher.byTag()
# of results
request
visualization
Radical
filter
hasAssay.
description
response
onClick()
description
HTML table
processing
JSON.
stringify(response)
color
d3.js scatter
graph
publishedUnits
Unit conversion
(x,y)
publishedValue
jquery.tipsy.js

9. search box and button
free radical target selection
activity unit selection
visualization options
data points with opacity
d3.js scatter plot
jquery.tipsy.js tips on mouseOver
units and scale change
description onClick
table with results

10. 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

11. Outlook - Combining results with food database
- Motivation for unification of units across OpenPHACTS database

12. Demo