activity of antioxidants against cancer target(s)
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/1.jpg)
Activity of Antioxidants Against Cancer Target(s)
Using the OpenPHACTS database and d3.js data visualization library
by Taís Ribeiro & Tim van de Goor
![Page 2: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/2.jpg)
Research QuestionWhat is the activity of antioxidants (present in the OpenPHACTS database) against different free radicals (e.g. a carcinogenic radical)?
![Page 3: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/3.jpg)
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
![Page 4: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/4.jpg)
Finding the right target moleculeMost common in OpenPHACTS results:- DPPH (a standard probing radical)- ABTS (a standard probing radical)
- Nitric Oxide- Peroxide- Superoxide
![Page 5: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/5.jpg)
Filtering the JSON results- Hardcoded exceptions:
![Page 6: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/6.jpg)
Unifying activity units- Selected %, uM and ug/mL as standard units- Conversion by hardcoded exceptions:
![Page 7: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/7.jpg)
(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
![Page 8: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/8.jpg)
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
![Page 9: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/9.jpg)
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
![Page 10: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/10.jpg)
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
![Page 11: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/11.jpg)
Outlook- Combining results with food database
- Motivation for unification of units across OpenPHACTS database
![Page 12: Activity of Antioxidants Against Cancer Target(s)](https://reader035.vdocument.in/reader035/viewer/2022062323/56816221550346895dd248c4/html5/thumbnails/12.jpg)
Demo