Emerging TechnologiesSemantic Web and Data Integration

This meeting will start at 5 min past the hourAs 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

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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

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Questions

• Use of the wiki for communication – any questions?

• Are we ready to move forward?• Feedback on meetings to date?

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A use case and short technical examples Python, SAS, RDFa

Marc Andersenmja@statgroup.dk

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. http://www.oreilly.com/catalog/9780596153816

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

datapoint-rdf.xmlrdfa-class.sas rdfa-class.html do2-rdfa-class.py

SAS Generated output with RDFa

Google Chrome extension - RDFa Triples Lister https://chrome.google.com/webstore/detail/rdfa-triples-lister/lmojbfnaigeibgkhacnebnpbhddpnoam

Roundtripping: Get the data usingSPARQL using RDFlib in Python

import rdflibfrom rdflib import pluginfrom rdflib.namespace import Namespacefrom rdflib.graph import Graphg = Graph()# change url to your serverurl= "http://s107:8000/rdfa-class.html"g.parse(location=url, format="rdfa" )

Result1 Alfred M 142 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 "name"@en . ?dpSex ds:Column "sex"@en . ?dpAge ds:Column "age"@en . ?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 HTTPThe 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 http://linkedscience.org/tools/sparql-package-for-r/linked-open-piracy-tutorial/

get-sparql9.sas

RDFa Content Editor - http://rdface.aksw.org/test/tinymce/examples/rdfaDemo.html

Ontologies

SKOS - Simple Knowledge Organization System RDF Schemahttp://www.w3.org/2004/02/skos/ http://www.w3.org/TR/2009/REC-skos-reference-20090818/

The RDF Data Cube Vocabularyhttp://www.w3.org/TR/2013/WD-vocab-data-cube-20130312/

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?