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 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

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

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

A use case and short technical examples Python, SAS, RDFa Marc Andersen 03-may-2013

Use Case Reviewer creates table by copy-paste of output with RDFa markup. Hovering over a cell with, say, N=42 provides the definition for count as a popup. In the popup clicking on the patients link opens a window showing the data listing for the corresponding 42 patients. Reviewer activates ”get data”, and the data are shown in a grid for further processing

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.

Creating RDFa using SAS Approach: Extend SAS html tagset to create RDFa using content and value properties in span tag Use SAS PROC report to make the output

SAS Generated output with RDFa Google Chrome extension - RDFa Triples Lister lister/lmojbfnaigeibgkhacnebnpbhddpnoam

Roundtripping: Get the data using SPARQL using RDFlib in Python import rdflib from rdflib import plugin from rdflib.namespace import Namespace from rdflib.graph import Graph g = Graph() # change url to your server url= " class.html" g.parse(location=url, format="rdfa" ) Result 1 Alfred M 14 2 Alice F 13 qres = g.query( """SELECT DISTINCT ?row ?nameVal ?sexVal ?ageVal WHERE { ?dpName ds:Row ?row. ?dpSex ds:Row ?row. ?dpAge ds:Row ?row. ?dpName ds:Column ?dpSex ds:Column ?dpAge ds:Column ?dpName ds:Value ?nameVal. ?dpSex ds:Value ?sexVal. ?dpAge ds:Value ?ageVal. }""", initNs=dict( ds=Namespace("datapoint-rdf.xml/") ) for row in qres.result: print("%s %s %s %s" % row)

SPARQL endpoint accessed using SAS SPARQL queries are performed over http. The query can be made using SAS PROC HTTP The results in xml format can be transformed into SAS data set using SAS XML libname. The program enclosed shows how it can be done – but is not ready for production. R: example for-r/linked-open-piracy-tutorial/ for-r/linked-open-piracy-tutorial/

RDFa Content Editor - aDemo.html aDemo.html

Ontologies SKOS - Simple Knowledge Organization System RDF Schema / The RDF Data Cube Vocabulary /

Looking forward Make/identify SAS tools? –And/or use other tools? Select ontology to present results –BRIDG? For the use case –browser based or dedicated application?