Linking clinical data standards

Linking Clinical Data Standards
Presented by Kerstin Forsberg
AstraZeneca R&D, Clinical Information Strategy
kerstin.l.forsberg@astrazeneca.com
kerfors on Twitter, LinkedIn, SlideShare, Blogspot, citulike

Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond 1

Things I want to show you
• Beyond a Web of Documents
 Web of Data
• Forerunners
 The UK and US Government
• Two things to remember
 Triples and Global Identifiers

• Three live examples
 From the Linking Open Data cloud


Things for CDISC, and for us in
the industry, to consider
• How this relates to the Innovative Medicine
Initiative (IMI) projects

• Pragmatic first steps for CDISC, together with NCI
 Linking Clinical Data Standards

• Opportunities across the industry
 Linking Clinical Study Metadata
 Linking Clinical Data


Acknowledgements
 Bosse Andersson, for sharing insights from AstraZeneca’s engagement in

Semantic Web Health Care and EU project The Large Knowledge Collider
Life Sciences (HCLS) Interest Group Linked Life Data
Linking Open Drug Data

 Wayne Kubick, CDISC and Oracle, for good email discussions last summer

 Martin Agfjord, Gothenburg University, for the Bachelor Thesis work

 Chimezie Ogbuji, Case Western Reserve University's Center for Clinical
Investigation and previously Cleveland Clinics, for the explorative work using
the Patient Controlled Health Records (PCHR) Ontology for Clinical Data

 Sam Hume, Simon Lundberg, Dan Ringenbach, Lee Evans,
Gunnar Magnusson for being ”healthy volunteers”


Web of Documents

Web 3.0

Image Source: Frederic Martin
Web of Data


Forerunners:
The UK and US Government

data.gov online “Open Government data.gov relaunch
January 1, 2009

December 8, 2009
“Openness will strengthen

May 21, 2010
May 21, 2009
our democracy and promote Directive” released 6.4 billion RDF triples
efficiency and effectiveness
in Government.”
--- President Obama

January 19, 2010
June30,2009

Putting
Government
Data online data.gov.uk online

Illustration by Prof .Jim Hendler
The Semantic Web 2010 Status Update


Linking Open Data cloud


What’s a Triple?
subject predicat object

An example from a text book

The sky has the color blue

Three example of facts from the Open Linked Data cloud
Payment number 8605670 netAmount 120.00
Clinical Trial number NCT00755378 enrollment 58
The Brussels Capital Region populationTotal 1080790

Three example representing some of the standards for these three facts
“The net amount of the payment. This is the effective cost to
The property netAmount comment the payer after any reclaimable tax has been deducted.”

The type of entity Active Ingredient subClassOf Type of entity Chemical Substance
The data property populationTotal domain Type of object Populated Place


And, what’s RDF? And, how is XML
related to this?
Common Model for Data

subject predicat object

Resource Description Framework

Alternative serialization formats


What’s a Global Identifier?
Linked Data Principles

1. Use URIs (Uniform Resource Identifiers)
to identify things.
.
2. Use HTTP URIs so that these things can be
referred to and looked up ("dereferenced") by
people and “machines”.
Three examples of identifiers from the Open Linked Data cloud
http://spending.lichfielddc.gov.uk/spend/8605670
http://data.linkedct.org/resource/trial/NCT00755378
http://dbpedia.org/resource/Brussels

Three examples of identifiers used in the standards behind the three examples
http://reference.data.gov.uk/def/payment#netAmount

http://www.w3.org/2001/sw/hcls/ns/transmed/TMO_0000
http://dbpedia.org/ontology/populationTotal


And, what’s the difference between
URI and URL?

Brussels Capital Region
is a “real world” entity Identified by this URI

Locator (URL) of the “people friendly” view of the
data about the Brussels Capital Region
http://dbpedia.org/page/Brussels

Linked Data Principles Locator (URL) of the “machine-processeable”
data about the Brussels Capital Region
3. Provide useful, structured, http://dbpedia.org/data/Brussels.rdf
information about the thing
when its URI is
lock-up:ed (de-referenced).


So, what’s the fourth Linked Data
principle?

http://data.nytimes.com/N78748399240553400231
owl:sameAs
owl:sameAs
http://sws.geonames.org/2800866/
Linked Data Principles

4. Include links to other, related
URIs in the exposed data to
improve discovery of other
related information.


Semantic Web standards is a key topic
across the IMI projects

Innovative Medicine Initiative

EHR4CR DDMoRE OpenPHACTS
Electronic Health Records Drug Disease Model The Open Pharmacological
for Clinical Research Resources Concepts Triple Store

RICORDO
Researching Interoperability using
Core Reference Datasets and
Ontologies for the Virtual
Physiological Human


Pragmatic first steps for CDISC,
together with NCI
• Learn from others, such as the UK and US
Government
• Apply the Linked Data principles
 Start with the SDTM CT:s e.g. the Trial Summary
Parameters
• Strive for a 5-star rating of Linked Open Data

Pragmatic first steps, more details


Opportunities across the industry
• Applying the four Linked Data principles for
 Linking Clinical Subject Data


A scenario:
Linking Clinical Study Metadata
Internal
categorization to
support Design &
Interpretation
decisions

http://clinial.data.astrazeneca.com/id/study/D8180C00011
owl:sameAs
http://data.linkedct.org/resource/trials/NCT00755378

What would we like to see on a
What would we likewebpage
internal to see as the
linked data description of data
presenting linked it?
describing a clinical study?

More ideas


So, why I'm so enthusiastic about
all of this!
• Well applied Linked Data principles and cautious
steps building on existing insights …
• … would improve the research utility of clinical
datasets
 Organized for associations
 Prepared for not yet defined use
 Ready for automation where computers can
function alongside us to
• Mitigate the complexity in clinical research
• Improve the productivity in clinical data
management
• …
Live examples Pragmatic first steps More ideas


Extras


Three Live Examples
1. Net amount for an expenditure from a local authority in UK
2. Enrollment number for a study from ClinicalTrial.gov
3. Population of Brussels Capital Region from Wikipedia

1 2 3

2 of 10 Triples 2 of 48 Triples 4 of 992 Triples

Three different approaches to standardization
Pragmatic first steps More ideas


Expenditure amount for a local
authority in UK
1


Expenditure amount for a local
authority in UK
1
Live view using the Web Data Inspector

2 of 10 Triples


An example of a top-down approach to
standardization for Linked Data
The Linked Data Cube Vocabulary


UK government: Top-down approach to
standardization for Spending Data
Statistical Data perspective
Linked Data Cube Vocabolary

Payment Ontology

Live example index


Enrollment number for a study
from ClinicalTrial.gov
2

Semantic Web Health Care
and Life Sciences (HCLS)
Interest Group

(Life Science part of the
Linking Open Data cloud)


Enrollment number for a study
from ClinicalTrial.gov
2


Interest Group

(Life Science part of the
Linking Open Data cloud)

2 of 48 Triples


An example of first using the source data
structure as the ”standard” …
2


2 of 48 Triples

Database key Variabel name Table name


… and then as a next step look for a
common standard
Live view using the Web Data Inspector and Life Sciences (HCLS)
Interest Group
Translational Medicine Ontology
(a.k.a. Pharma Ontology)

Live example index


Population of Brussels Capital
Region from Wikipedia
3



Linking between different sources about
the same entity using different identifiers
3



Bottom-up standardization: Community
curated, and a central shallow Ontology

http://dbpedia.org/ontology/PopulatedPlace
http://dbpedia.org/ontology/populationTotal
http://dbpedia.org/ontology/populationAsOf


Pragmatic first steps for CDISC,
together with NCI
• Learn from others, such as the UK and US
Government
• Apply the Linked Data principles
 Start with the SDTM CT:s e.g. the Trial Summary
Parameters
• Strive for a 5-star rating of Linked Open Data


Linked Open Data star scheme


Pragmatic first steps
Learn from others, two examples
• AGFA
 Clinical drug administration forms mapped to SNOMED
CT and FDA codes using the SKOS (Simple Knowledge
Organization System) vocabulary
http://www.agfa.com/w3c/2009/drugAdministrationForms#

• EU Project – LarKC
• Published CDISC CT:s as part of Linked Life Data
http://linkedlifedata.com/resource/umls/id/C1879952
http://linkedlifedata.com/resource/umls/id/C0013153


Pragmatic first steps, start with
Trial Summary Parameters
0 Existing text strings published in a long file in Excel txt format (soon also as ODM/XML)


1 Establish a CDISC URI scheme
Proposal: Build on http://data.gov.uk/resources/uris
Examples:
http://reference.data.cdisc.org/ct/sdtm/ROUTE#ORAL
or alt. using the C-code from NCI Thesaurus
http://reference.data.cdisc.org/ct/sdtm/C66729#C38288

2 Model CDISC SDTM CT:s as RDF Triples


1 Establish a CDISC URI scheme
Examples:
http://reference.data.cdisc.org/ct/sdtm/ROUTE#ORAL
or alt. using the C-code from NCI Thesaurus
http://reference.data.cdisc.org/ct/sdtm/C66729#C38288

2 Model CDISC SDTM CT:s as RDF Triples 3
Publish in RDF/XML

4
De-reference/look-up service so people
and applications can get descriptions of
individual code lists and code.

5
Create a so called SPARQL endpoint so that CDISC
standards published as triples can be queried
directly using the RDF query language.


Some thoughts and ideas explored
• Applying the four Linked Data principles
• A scenario
• Explore the use of
– BRIDG Domain Model (to be published in OWL/RDF)
– Translational Medicine Ontology - TMO

 Linking Clinical Data
• Best practice for URI scheme and minting URI:s
• Explorative work: using the Computer-Based
Patient Record (CPR) Ontology for Clinical Data


A scenario:
Linked Clinical Study Metadata
Internal
categorization to
support Design &
Interpretation
decisions

http://clinial.data.astrazeneca.com/id/study/D8180C00011
owl:sameAs
http://data.linkedct.org/resource/trials/NCT00755378

What would we like to see on a
What would we likewebpage
internal to see as the
linked data description of data
presenting linked it?
describing a clinical study?

More ideas


Explore the use of BRIDG and TMO
for common classes and properties

Interest Group
Translational Medicine Ontology


Linking Clinical Data: Explore URI
scheme and minting URI:s



Explorative work: using the Computer-Based
Patient Record (CPR) Ontology for Clinical Data

Acknowledgements:
Chimezie Ogbuji, Case Western Reserve University's Center for
Clinical Investigation, previously Cleveland Clinics.
Martin Agfjord, IT University, Göteborg

If you want to learn more
An Intro To The Semantic Web: Why You Need To http://data.gov.uk/linked-data
Know About It Sooner Than Later , by Samantha Wong
Image Source: Frederic Martin http://www.data.gov/semantic

The Semantic Web 2010 Status Update
by Prof .Jim Hendler

Open data: accountability, citizen utility
and economic opportunity.

Linked Spending Data –
How and Why Bother

Guide to the
Payments Ontology How DBpedia Treats Linked Open Data star scheme by example
Wikipedia as a Database
Presentation: Linking Open Drug Data
Statistical Data in RDF Interest Group for Semantic Web in
Health Care and Life Science
The RDF Data Cube http://www.w3.org/blog/hcls
vocabulary

The Linking Open Data
cloud diagram

Excellent article “More than Words: Biomedical Ontologies”


And now – An Evening with TinTin
at the Brussels Comic Strip Center!


Linking clinical data standards

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