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Semantic Technology 101 for Pharma
Semantic Technology 101 for Pharma PhUSE CSS Sunday, 13 March 2016 7:30pm – 9:30pm (after opening session)
Tim Williams UCB BioSciences Inc, USA [email protected]
Marc Andersen Stat Group ApS, Denmark [email protected]
Co-‐leads: Analysis Results & Metadata Project
Workshop Outline A Pragmatic Introduction to the Semantic Web • Background and Importance to Pharma • Technologies & Toolsets • Resource Description Framework (RDF) • Querying with SPARQL • Creating RDF • Uploading and Serving RDF • Visualizing & Traceability • PhUSE CS Working Group Projects
Collected Data
Clinical Program Design in RDF
Study Design and Protocol in RDF
CDISC Founda8onal Standards in RDF
Analysis Results & Metadata
Regula8ons and Guidances in RDF
Data Lifecycle
CS WG Linked Data Projects & Deliverables
Clinical Development
Plan
Analysis Results & Displays
Study Protocol
Study Design
CSR Submission
Tabulated Data
Analysis Data
Eligibility Criteria in RDF
Reference: hLp://bnode.org/blog/2009/07/08/the-‐seman4c-‐web-‐not-‐a-‐piece-‐of-‐cake
Core Concepts • All things have a name • All names are unique and addressable
– HTTP URI’s • Things are linked
– Directed graphs • Links have meaning
– Seman4cs
Born in the web, Applica4on beyond the web.
Resource Description Framework (RDF)
Drug X has_side_effect dry mouth
Turtle (Terse RDF Triple Language) @prefix drug: <http:/pharmCo.com/drug/> . @prefix ont: <http:/pharmCo.com/ontology/> . @prefix clin: <http:/pharmCo.com/clinObs/> . drug:DrugX ont:has_side_effect clin:dryMouth .
Directed Graph Triple
Mighty oaks from little acorns grow.
ds:obs1 a qb:Observation ; dim:sex code:sex-F; dim:treat code:trt-Placebo; dim:race code:race-_ALL_; dim:stat code:stat-count; meas:measure "12"^^xsd:int; qb:dataSet ds:dataset-DM .
Representation. Visualization. Interaction. Baseline Placebo LowDose HighDose Characteristic N=28 N=30 N=29 ---------------------------------------------------------------------- Sex F 12 (42.9) 14 (46.7) 16 (55.2) M 16 (57.1) 16 (53.3) 13 (44.8)
ds:obs1 a qb:Observation ; dim:sex code:sex-F ; dim:treat code:trt-Placebo ; dim:race code:race-_ALL_ ; dim:stat code:stat-count ; meas:measure "12"^^xsd:int ; qb:dataSet ds:dataset-DM .
Interactive Summary Tables
Why Learn about the Semantic Web? • Integrate diverse data sources • Multi-dimensional data models • Integrated metadata & Context • Leverage existing standards
– CDISC Standards in RDF • Analysis Results as RDF • CSR
– Production – Hyperlinks between text, tables, and listings – Enhanced review
• Data exploration and visualization
• Reliability and Trust
Workshop Prerequisites • No previous experience required • Laptop (Attendee survey re. Administrator privileges?)
• Applications* – R (with rrdf package) or SAS – Virtuoso Open Source Edition – Local web service (Python, Apache, WAMP…)
* Recommended but not mandatory for attendance. Installation and configuration instructions will be provided in the days prior to the conference
Registration • Pre-registration is required. – CSS Conference Registration page – Other?
“We hope to see you there!”
- Tim & Marc
