Using the OpenPHACTS database and d3js data visualization library by Taís Ribeiro amp Tim van de Goor Research Question What is the activity of antioxidants present in the OpenPHACTS database against ID: 423602
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Slide1
Activity of Antioxidants Against Cancer Target(s)
Using the OpenPHACTS database and d3.js data visualization library
by Taís Ribeiro & Tim van de Goor Slide2
Research Question
What is the activity of antioxidants (present in the OpenPHACTS database) against different
free radicals (
e.g.
a carcinogenic radical)? Slide3
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 librarySlide4
Finding the right target molecule
Most common in OpenPHACTS results: - DPPH (a standard probing radical)
- ABTS (a standard probing radical)
- Nitric Oxide
- Peroxide
- SuperoxideSlide5
Filtering the JSON results
- Hardcoded exceptions:Slide6
Unifying activity units
- Selected %, uM and ug/mL as standard units- Conversion by hardcoded exceptions:Slide7
(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 resultsSlide8
Code execution
conceptSearcher
.byTag()
compoundSearcher
.compound
Pharmacology
Count()
compoundSearcher.
compound
Pharmacology()
conceptURI
conceptURI
# of results
JSON.
stringify(response)
response
hasAssay.
description
publishedUnits
publishedValue
Unit conversion
Radical
filter
d3.js scatter
graph
description
(x,y)
color
jquery.tipsy.js
onClick()
visualization
processing
request
input
HTML tableSlide9
search box and button
free radical target selection
activity 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 onClickSlide10
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 Slide11
Outlook
- Combining results with food database- Motivation for unification of units across OpenPHACTS databaseSlide12
Demo