1.
Linked Data efforts for data standards in
biopharma and healthcare
Kerstin Forsberg (@kerfors on Twitter, SlideShare etc.)
Informatics Analyst and Lifetime Learner
AZ IT | R&D Information
Länkade Data i Sverige 2016, LDSV2016
See also
http://kerfors.blogspot.se/2016/04/linked-data-in-
sweden-2016.html

2.
”Standardized the Standards”
In traditional standard organizations
• CDISC in RDF
• HL7 FHIR in RDF
• MeSH in RDF
• ICD-11 in OWL
• Others standards e.g. ATC, WHO Drug and
MedDRA
2 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

3.
Use standardized standards
3
Web of (Linked) Data
An Intro To The Semantic Web: Why You Need To
Know About It Sooner Than Later , by Samantha Wong
Image Source: Frederic Martin
Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information
http://yosemiteproject.org/
In new cross-functional communities

4.
”Standardized the Standards”
Observations
• Pushing back to traditional standard
organizations requires knowledge awareness
and community building
• Much of the work done in new cross-
functional communities e.g. Yosemite project
and PhUSE
• Many use github
• Excel spreadsheets still rules :-(
4 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

5.
• CDISC2RDF, Oct 2012 a pre-competitive project with
AZ, Roche, W3C et al. to show case Semantic Web
standards and Linked Data principles.
• FDA meeting Nov 2012: Solutions for Study Data
Exchange Standards Meeting – W3C Semantic Web
presentation.
• June 2013 the Semantic Technology project,
a FDA/PhUSE working group for Emerging
Technologies, with 25+ repr. from FDA,
CDISC, Pharma:s, CRO:s and software vendors.
• Oct 2013 press release: Representing
existing standards (SDTM, CDASH,
SEND, ADaM) in RDF.
• Dec 2014, Public review of CDISC in RDF Guide.
• July 2015, Published on http://www.cdisc.org/rdf and
https://github.com/phuse-org/rdf.cdisc.org
CDISC (clinical study data standards) in RDF
Knowledge awareness and community building
5
CDISC Interchange Europe 2011 and 2012
presentations from Roche and AstraZeneca
Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

6.
6 Kerstin Forsberg | WHO UMC, Jan 21 2015 AZIT | R&D Information
CDISC in RDF
From Human Readable to Machine Processable
RDF triples describing one variable/data element
and linking to related standard parts

7.
MeSH in RDF
Example http://id.nlm.nih.gov/mesh/D015242
for Ofloxacin in MeSH

8.
ICD-11 in OWL
iCAT tool, but Excel spreadsheets still rules :-(
8 Author | 00 Month Year Set area descriptor | Sub level 1

9.
“Pushing back” to get MedDRA in RDF
AZ Vocabulary Management team shared this with MedDRA MSSO
9
Courtland Yockey, Informatics Analyst
AstraZeneca R&D Information, USA
A very simple SKOS-rendering
of MedDRA
• term  skos:Concept
• hierarchy level 
skos:ConceptScheme
• SMQ  skos:Collection
Approach should be augmented with
VoID representation of MedDRA
versions and term properties
distinguishing active from inactive
terms.
Skos:Collection is likely not sufficient
to support SMQ versioning nor
context of terms in an SMQ (e.g.
weight)
Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

10.
“Pushing back” to get ATC codes in RDF
AZ Vocabulary Management team created a RDF representation of
ATC codes using the SKOS Schema
10
Courtland Yockey, Informatics Analyst
AstraZeneca R&D Information, USA
4 example RDF Triples
representing part of a ATC code
Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

11.
”Standardized the Standards”
Observations
• Pushing back to traditional standard
organizations requires knowledge awareness
and community building
• New cross-functional communities e.g.
Yosemite project and PhUSE
• Many use github
• Excel spreadsheets still rules :-(
11 Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information

12.
Semantic Web
Standards
 A stack of standards to
represent data and semantics
based on Resource
Description Framework
(RDF). RDF is a framework
for creating statements in a
form of so-called triples
 OWL and SKOS: RDF-based
standards to represent
vocabularies of terms
representing identified entities
and concepts
 SPARQL: query language for
RDF triples
Building Linked Data
Applications
 Use of Semantic Web
standards and Linked Data
principles enabling us to ask
questions and solve business
problems across a
heterogeneous information
landscape across open and
closed sources
Capture
Business
Questions and
Sources
Domain
Expert
Concept Map
Build Formal
Ontolog!
Challenge
with Linked
Open Data
Model
Business
Questions
(SPARQL)
Interact with
RDF answer
in a Faceted
Browser
Web of Data
Open and Closed
 Open data sources applying
the Linked Data principles
and semantic web standards
as a Web of Data
 Central is the Wikipedia’s
structured content via
DBpedia used by e.g.
Google’s KnowledgeGraph
and IBM’s Watson.
 Closed data sources now
also form internal Webs of
Data
Linked Data
Principles
 Use URIs (Uniform Resource
Identifiers) as names for
things.
 Use HTTP URIs so that
people can look up
(dereference) those names.
 When someone looks up a
URI, provide useful
information.
 Include links to other URIs so
that they can discover more
things
Linked Data in One slide
Kerstin Forsberg | LDSV2016, April 26 2016 AZIT | R&D Information