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Emerging Technologies

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Emerging Technologies. Semantic Web and Data Integration This meeting will start at 5 min past the hour As a reminder, please place your phone on mute unless you are speaking. 3 May 2013. Emerging Technologies. Semantic Web and Data Integration. 3 May 2013. Meeting Agenda.

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  1. Emerging Technologies Semantic Web and Data Integration This meeting will start at 5 min past the hour As a reminder, please place your phone on mute unless you are speaking 3 May 2013

  2. Emerging Technologies Semantic Web and Data Integration 3 May 2013

  3. Meeting Agenda Update- Discussion with related initiatives CDISC Collaboration OpenCDISC validation checks in RDF NCI-EVS publication of Controlled Terminology in RDF Folding the CDISC2RDF work into FDA/PhUSE ST Project Moving Forward – Formation of sub-teams Focus of our next meeting (10 May 2013) Presentation - Marc Andersen (StatGroup) A use case and short technical examples Python, SAS, RDFa 2

  4. Formation of sub-teams Propose to focus on the development of use cases CDASH version 1.1 SDTM Version v1.3/IG v3.1.3, TA Supplements – Expand RDF representation of SDTM v1.3/IG v3.1.2 ADaM Need to identify leads Consider which area that you would want to focus on Respond to discussion thread on wiki by 16 May 2013 3

  5. Questions Use of the wiki for communication – any questions? Are we ready to move forward? Feedback on meetings to date? 4

  6. A use case and short technicalexamplesPython, SAS, RDFa Marc Andersen mja@statgroup.dk 03-may-2013

  7. Use Case Reviewercreatestable by copy-pasteof output with RDFamarkup. Hovering over a cell with, say, N=42 provides the definition for count as a popup. In the popupclicking on the patients link opens a windowshowing the data listing for the corresponding 42 patients. Revieweractivates ”get data”, and the data areshown in a grid for furtherprocessing

  8. RDFa and Python I learned a lot from reading and trying the examples in: “Programming the Semantic Web” by Toby Segaran, Colin Evans, and Jamie Taylor. http://www.oreilly.com/catalog/9780596153816

  9. CreatingRDFausing SAS Approach: Extend SAS html tagset to createRDFausingcontent and value properties in span tag Use SAS PROC report to make the output

  10. SAS Generated output with RDFa Google Chrome extension - RDFaTriples Lister https://chrome.google.com/webstore/detail/rdfa-triples- lister/lmojbfnaigeibgkhacnebnpbhddpnoam

  11. qres = g.query( """SELECT DISTINCT ?row ?nameVal ?sexVal ?ageVal WHERE { ?dpNameds:Row ?row . ?dpSexds:Row ?row . ?dpAgeds:Row ?row . ?dpNameds:Column "name"@en . ?dpSexds:Column "sex"@en . ?dpAgeds:Column "age"@en . ?dpNameds:Value ?nameVal . ?dpSexds:Value ?sexVal . ?dpAgeds:Value ?ageVal . }""" , initNs=dict( ds=Namespace("datapoint-rdf.xml/") ) ) for row in qres.result: print("%s %s %s %s" % row) Roundtripping: Get the data usingSPARQL usingRDFlib in Python Result 1 Alfred M 14 2 Alice F 13 import rdflib from rdflib import plugin from rdflib.namespace import Namespace from rdflib.graph import Graph g = Graph() # change url to your server url= "http://s107:8000/rdfa-class.html" g.parse(location=url, format="rdfa" )

  12. SPARQL endpointaccessedusing SAS SPARQL queriesareperformed over http. The querycanbe made using SAS PROC HTTP The results in xml format canbetransformedinto SAS data set using SAS XML libname. The program enclosed shows how it canbe done – but is not ready for production. R: examplehttp://linkedscience.org/tools/sparql-package-for-r/linked-open-piracy-tutorial/

  13. RDFaContent Editor - http://rdface.aksw.org/test/tinymce/examples/rdfaDemo.html

  14. Ontologies SKOS - Simple Knowledge Organization System RDF Schema http://www.w3.org/2004/02/skos/ http://www.w3.org/TR/2009/REC-skos-reference-20090818/ The RDF Data Cube Vocabulary http://www.w3.org/TR/2013/WD-vocab-data-cube-20130312/

  15. Looking forward • Make/identify SAS tools? • And/or useothertools? • Select ontology to present results • BRIDG? • For the use case • browser based or dedicatedapplication?