Create RDF using R - PhUSE Wiki · 34 Who We Are Marc works as statistician and often ends...
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1 Create RDF using R • R with rrdf, rrdflibs https://github.com/egonw/rrdf • R Data frame to RDF – Excel->data frame-> to RDF – SAS dataset -> data frame -> RDF rrdf, rrdflibs
Transcript of Create RDF using R - PhUSE Wiki · 34 Who We Are Marc works as statistician and often ends...
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Create RDF using R
• R with rrdf, rrdflibs
https://github.com/egonw/rrdf
• R Data frame to RDF
– Excel->data frame-> to RDF
– SAS dataset -> data frame -> RDF
rrdf, rrdflibs
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Create RDF using R
Packages: rrdf, rrdflibs • add.triple()
– Add a triple :object is a URI
• add.data.triple()
– Add triple: object is a literal
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Create RDF using R
Try or follow along
File: createTTLFromR.R
Output File: createTTLFromR.TTL
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Create RDF using SAS
• SAS accessing SPARQL service using PROC HTTP • All functions provided by the service, see SPARQL 1.1 Protocol
(https://www.w3.org/TR/sparql11-protocol/)
• Implemented as SAS macros https://github.com/MarcJAndersen/SAS-SPARQLwrapper
• SAS generating text files with • RDF in Turtle
• SPARQL INSERT statements
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Output File:
createTTLFromSAS.TTL
Create RDF using SAS
Try or follo
w along
File: createTTLFromSAS.SAS
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Putting it all together
Extract, Transform
RDF Linked Data
Knowledgebase
Load
Federated Queries
• Analysis • Visualization • Submission • Publication
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• Introduction to Semantic Web & Linked Data
• Resource Description Framework (RDF)
• Pharma: Use and Impact
• Visualizing Linked Data
• PhUSE CSS Projects
• Conclusion
Outline
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“The choice for all major content providers is not whether to adopt a linked data approach but when. Asking ‘do we need linked data?’ today may be analogous to asking ‘do we really need a website?’ 15 years ago. ” - Cochrane Technical Report (2013)
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Traceability: THE Linked Data Super Power
Analysis Results & Displays
Study Protocol CSR Submission Data
Pharma Company, Biotech …
Regulatory Agency, Reviewer…
• Publications • Registries • Data Gathering
• Meta-analyses • Competitive
Intelligence
PRODUCE
CONSUME
Collected Data
Clinical Program Design in RDF
Study Design and Protocol in RDF
CDISC Foundational Standards in RDF
Analysis Results & Metadata
Regulations 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
Use Cases
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Web Standards meet Pharma Standards
• CDASH 1.1
• SDTM 1.2 + Impl. Guide 3.1.2
• SDTM 1.3 + Impl. Guide 3.1.3
• SEND Impl. Guide 3.0
• ADaM 2.1 + Impl. Guide 1.0
• Controlled Terminology
• CDISC e-share! (October 2014)
CDISC RDF - http://www.cdisc.org/rdf, https://github.com/phuse-org/rdf.cdisc.org
GetSDTM-DM-definition.rq
queryLocalCDISC.sas
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"I want to take the clinical trials results..."
"..and put them in an RDF Data Cube!"
Placebo LowDose HighDose
Baseline N=28 N=30 N=29
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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:treat code:trt-Placebo ; dim:sex code:sex-F ; dim:procedure code:procedure-count ; meas:measure "12"^^xsd:int ; qb:dataSet ds:dataset-DM . ds:obs2 a qb:Observation ; ...
Analysis Results & Metadata (WG)
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• Details at the Analysis Results & Metadata Working Group Breakout sessions.
RDF Data Cube for Clinical Trials Results
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• Introduction to Semantic Web & Linked Data
• Resource Description Framework (RDF)
• Pharma: Use and Impact
• Visualizing Linked Data
• Summary & Conclusion
Outline
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• Interactive tables and text
• Visualization as Entry Point
• D3js
• Examples
Visualizing Linked Data
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Interactive Tables, Text
SimpleDM Table
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• Linked Data = data and metadata traversal at no
extra cost!
Visualization as Entry Point
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D3js
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Trials: Interactive Gantt LINK
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Studies to Pool
LINK
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• Introduction to Semantic Web & Linked Data
• Resource Description Framework (RDF)
• Pharma: Use and Impact
• Visualizing Linked Data
• Summary & Conclusion
Outline
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Why Linked Data Traceability & Trust
Across the data lifecycle
Reuse
Exploration
Flexible content presentation
Reduce vendor Lock-in
Improve interoperability and data integration
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Why Linked Data • Integrated metadata
“Metadata is a love note to the people and machines after you.”- Jason Scott via Twitter, 2011
• Data + Metadata = Context • Semantic Search
• Find related drugs, targets, studies, adverse events
• Predictions • Feed into risk-based methods for study design and conduct
Build a Knowledge Base, not another data store!
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Learning Resources • PhUSE Wiki “Semantic Technology Working Groups”
http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology
• PhUSE Wiki “Semantic Technology Curriculum” http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology_Curriculum
• White papers, publications, presentations.
• “Learning SPARQL” by Bob DuCharme http://www.learningsparql.com/index.html - examples for download
• Semantic University by Cambridge Semantics http://www.cambridgesemantics.com/semantic-university
• RDF Primer http://www.w3.org/TR/2014/NOTE-rdf11-primer-20140624/
• Knowledge Engineering with Semantic Web Technologies 2015 https://open.hpi.de/courses/semanticweb2015
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Thank you
and Enjoy the Conference!
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Who We Are Marc works as statistician and often ends reproducing or extending earlier reporting, and thereby appreciates traceability from results to the data generation. With a strong urge to make and appreciate (complex) systems linked data is an interesting avenue. Marc has been co-chair for the AR&M group. For this workshop Marc has discussed the overall structure, and provided a few (technical) slides.
Tim is a Statistical Systems Analyst at UCB Biosciences. His interest in Linked Data was piqued at the PhUSE 2013 conference in Brussels. He currently co-chairs the AR&M project with Marc and serves as a co-lead of the PhUSE Semantic Technology Working Group. For this workshop Tim produced the slide deck and D3.js visualizations.
@NovasTaylor
@MarcJuAndersen
