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

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Presentation on theme: "Activity of Antioxidants Against Cancer Target(s) Using the OpenPHACTS database and d3.js data visualization library by Taís Ribeiro & Tim van de Goor."— Presentation transcript:

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 1.Finding the right target molecule (free radical) 2.Filtering the JSON results from OpenPHACTS API call 3.Unifying activity units (%, M, g/L) 4.Linking antioxidants to food sources 5.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 conceptSearcher. byTag() compoundSearcher.c ompound Pharmacology Count() compoundSearcher.c ompound Pharmacology() 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 table

9 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 onClick

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


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