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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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Emerging technologies

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 technologies1

Emerging Technologies

Semantic Web and Data Integration

3 May 2013


Meeting agenda

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

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


Questions

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

A use case and short technicalexamplesPython, SAS, RDFa

Marc Andersen

[email protected]

03-may-2013


Use case

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


Rdfa and python

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

CreatingRDFausing SAS

Approach:

Extend SAS html tagset to createRDFausingcontent and value properties in span tag

Use SAS PROC report to make the output


Sas generated output with rdfa

SAS Generated output with RDFa

Google Chrome extension - RDFaTriples Lister

https://chrome.google.com/webstore/detail/rdfa-triples-

lister/lmojbfnaigeibgkhacnebnpbhddpnoam


Roundtripping get the data using sparql using rdflib in python

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" )


Sparql endpoint accessed using sas

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/


Rdfa content editor http rdface aksw org test tinymce examples rdfademo html

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


Ontologies

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/


Looking forward

Looking forward

  • Make/identify SAS tools?

    • And/or useothertools?

  • Select ontology to present results

    • BRIDG?

  • For the use case

    • browser based or dedicatedapplication?


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