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Activity of Antioxidants Against Cancer Target(s)

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.

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Activity of Antioxidants Against Cancer Target(s)

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  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 compoundSearcher.compound Pharmacology Count() conceptURI compoundSearcher.compound Pharmacology() conceptURI input conceptSearcher.byTag() # of results request visualization response Radical filter hasAssay. description description onClick() 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. What’s not working: - Search suggestions - Error handling (partially) Difficulties: - Graph and axes layout - Server problems, changes in JSON formatting 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)

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

  12. Demo

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