This document discusses using RDF and linked data principles to display clinical trial results as interactive graphs and summary tables. It describes how RDF triples can represent clinical data and be rendered as directed graphs using D3.js. It also presents an interface with actions like "Describe", "Dimensions", and "Data" that build and display SPARQL queries of an RDF data cube, allowing linked exploration and visualization of results. Ongoing work in the PhUSE Semantic Technology Project aims to further specify the RDF data cube model and develop supporting R packages and documentation.

1. ‘Dude, where’s my graph?’
RDF Data Cubes for Clinical Trials
Data.
PhUSE 2015, Vienna
Part I: Graphing RDF with D3.js
Tim Williams,
UCB BioSciences Inc, USA
tim.williams@ucb.com
Part 2: Interactive Summary Tables
Marc Andersen
Stat Group ApS, Denmark
mja@statgroup.dk

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RDF Triples as Directed Graphs
Subject
predicate
Object
Vienna 1805681
populationTotal

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The Reality
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Dude,
where’s my graph?

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Clinical Trials Results: RDF Data Cube
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Dude,
seriously!!

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Using R to obtain and graph triples
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rrdf, rrdflibs networkD3
rrdf, rrdflibs jsonLite (HTTP server)

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Data Visualization with D3.js (d3js.org)
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Federated Query Visualization
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Webm Link
LiveGraph

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RDF Data Cube: High-Level Structure
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Webm link
LiveGraph

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RDF Data Cube: qb:Observation Model
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Webm Link
LiveGraph

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RDF Data Cube: Demographics
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Websm Link
LiveGraph

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RDF Code Lists Interactive Visualization
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webSM Link
LiveGraph

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But there is more
than graphs!
Everything is a
graph!

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Presented by Marc Andersen, StatGroup ApS
Part II : Interactive Summary Tables
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The interface
• Left side: Actions
• Right side: Results
• Build using HTML and javascript
• Shows HTML pages using iframe
• SPARQL queries to a triple store
• Rendition of SPARQL query results
• RDF data cube created in R
• HTML version of cube in row-column
format with href corresponding to the
underlying RDF object
• Drag and drop links to the actions on
the left
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Action: Describe
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Shows result of SPARQL query describe for the item dropped
Using OpenLink Virtuoso - HTTP based Linked Data Server, include SPARQL
endpoint
Virtuoso provides a faceted browser
Note Linked Data Server specific – other servers can be used, or other ways of
displaying the result.

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Action: Describe
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Action: Dimensions
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Dropping an observation
• shows all dimensions with code lists
Dropping a dimension
• shows only the dimension
Result of a SPARQL query displayed as
the html
returned from the SPARQL endpoint
(Virtuoso)

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Action: Dimensions
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Action: Data
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Dropping an observation
• Builds SPARQL query to retrieve underlying data using JavaScript
• Present received data as a table using JavaScript
• Drag URI to Action describe to invoke faceted browser
Instead of showing a table, the data can be visualized using, say, d3js

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Action: Data
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Action: Copy
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Dropping an observation
• copies the text representation and the URI for the object to the clipboard
• pasted into any application understanding text/HTML, e.g. Microsoft Word
Technical issue: have to use Ctrl-C to copy to clipboard. Clipboard functionality is defined in HTML5, but
works slightly different in each browser. So may need a specialized browser?

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Action: Copy
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Ongoing in PhUSE Semantic Technology Project
Technical specification of the cube
model
• In Draft 1 – July 31, 2015. Review and
discussion ongoing
R package
• Rewrite to match Tech Spec Draft 1, split
into smaller packages, move to
PhUSE.org GitHub
White Paper for considerations and
benefits of modeling Analysis Results
& Metadata in RDF
• Draft written, in process
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Analysis Results Model – see
http://www.phusewiki.org/wiki/index.php?title=Analysis_Results_Model
Modeling Analysis Results & Metadata to
Support Clinical and Non-Clinical Applications
New Project suggestions:
Concise specification of tables for
descriptive statistics using metadata –
inspiration for syntax/formular from
SAS PROC Tabulate
R packages tables (https://cran.r-
project.org/web/packages/tables/index.
html)
Tabular representation for inclusion in
CSR of analysis results using meta
data

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Conclusion
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* Display graphs * Present tables
Linked data methods are feasible
Interactive summary tables
• Possible to use linked data principles
when reporting clinical data
• Facilitates traceability – a URI for
each result provides context
• Potential to enhance both creation
and review of CSR
Graphs and visualization
• Offers new perspectives and possibilities for
data presentation
• Technically interesting & visually appealing
• Scale: more data sources can be combined and
presented
• Visualization and linked data goes well together
• Visualization as an entry point to exploration

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Thank you!
Part I: Graphing RDF with D3.js
Tim Williams,
UCB BioSciences Inc, USA
tim.williams@ucb.com
Part 2: Interactive Summary Tables
Marc Andersen
StatGroup ApS, Denmark
mja@statgroup.dk