Linking clinical data standards

Kerstin Forsberg CDISC Interchange Europe 2011 eHR and the World Beyond


Presented by Kerstin Forsberg

AstraZeneca R&D, Clinical Information Strategy

[email protected]

kerfors on Twitter, LinkedIn, SlideShare, Blogspot, citulike

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Linking Clinical Data Standards



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

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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

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Acknowledgements

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

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”

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Semantic Web Health Care and

Life Sciences (HCLS) Interest Group

Linking Open Drug Data

EU project The Large Knowledge Collider

Linked Life Data



Web of Data

Web 3.0

Web of Documents

Image Source: Frederic Martin

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http://fredericmartin.typepad.com/myblog/2007/11/from-web10-to-w.html



Forerunners:

The UK and US Government

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Ja

nu

ary

1,

20

09

“Openness will strengthen

our democracy and promote

efficiency and effectiveness

in Government.”

--- President Obama

Putting

Government

Data online

Ma

y 2

1, 2

00

9

Ja

nu

ary

19

, 2

01

0

data.gov.uk online

Ma

y 2

1, 2

01

0

data.gov online data.gov relaunch

6.4 billion RDF triples

Ju

ne

30,2

009

Dece

mb

er

8,

20

09

“Open Government

Directive” released

Illustration by Prof .Jim Hendler

The Semantic Web 2010 Status Update

http://www.google.com/imgres?imgurl=http://weblogmania.files.wordpress.com/2009/03/tim-berners-lee.jpg&imgrefurl=http://weblogmania.wordpress.com/2009/03/16/tum-zamanlarin-en-unlu-10-hackeri/&usg=__0mfX4nw3vNhFjE1UZV2uCKr8XkE=&h=338&w=450&sz=41&hl=en&start=10&um=1&itbs=1&tbnid=EAtcXTNQczINNM:&tbnh=95&tbnw=127&prev=/images?q=tim+berners+lee&um=1&hl=en&client=firefox-a&sa=N&rls=org.mozilla:en-US:official&tbs=isch:1

http://www.cs.rpi.edu/~hendler/


http://www.slideshare.net/jahendler/the-semantic-web-2010-update-5673441




Linking Open Data cloud

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What’s a Triple?

subject predicat object

has the color The sky blue

netAmount Payment number 8605670 120.00

enrollment Clinical Trial number NCT00755378 58

populationTotal The Brussels Capital Region 1080790

comment The property netAmount “The net amount of the payment. This is the effective cost to

the payer after any reclaimable tax has been deducted.”

subClassOf The type of entity Active Ingredient Type of entity Chemical Substance

domain The data property populationTotal Type of object Populated Place

An example from a text book

Three example of facts from the Open Linked Data cloud

Three example representing some of the standards for these three facts

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And, what’s RDF? And, how is XML

related to this?

subject predicat object

Common Model for Data

Resource Description Framework

Alternative serialization formats

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What’s a Global Identifier?

http://spending.lichfielddc.gov.uk/spend/8605670

http://data.linkedct.org/resource/trial/NCT00755378

Three examples of identifiers from the Open Linked Data cloud

Three examples of identifiers used in the standards behind the three examples

http://dbpedia.org/resource/Brussels

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”.

http://reference.data.gov.uk/def/payment#netAmount

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

http://dbpedia.org/ontology/populationTotal

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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

Locator (URL) of the “machine-processeable”

data about the Brussels Capital Region

http://dbpedia.org/data/Brussels.rdf


3. Provide useful, structured,

information about the thing

when its URI is

lock-up:ed (de-referenced).

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http://dbpedia.org/data/Brussels.rdf



So, what’s the fourth Linked Data

principle?


4. Include links to other, related

URIs in the exposed data to

improve discovery of other

related information.


http://data.nytimes.com/N78748399240553400231

http://sws.geonames.org/2800866/

owl:sameAs

owl:sameAs

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Semantic Web standards is a key topic

across the IMI projects

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Innovative Medicine Initiative

OpenPHACTS

The Open Pharmacological

Concepts Triple Store

DDMoRE

Drug Disease Model

Resources

EHR4CR

Electronic Health Records

for Clinical Research

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

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Pragmatic first steps, more details



Opportunities across the industry

• Applying the four Linked Data principles for


Linking Clinical Subject Data

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Internal

categorization to

support Design &

Interpretation

decisions

A scenario:


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http://clinial.data.astrazeneca.com/id/study/D8180C00011

http://data.linkedct.org/resource/trials/NCT00755378

What would we like to see as the

linked data description of it?

What would we like to see on a

internal webpage

presenting linked data

describing a clinical study?

owl:sameAs

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

• …

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Pragmatic first steps More ideas Live examples



Extras

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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

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

Three different approaches to standardization

1 2 3

Pragmatic first steps More ideas



Expenditure amount for a local

authority in UK

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1



Expenditure amount for a local

authority in UK

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Live view using the Web Data Inspector

2 of 10 Triples

1

http://inspector.sindice.com/inspect?url=http://spending.lichfielddc.gov.uk/spend/8605670&content=



An example of a top-down approach to

standardization for Linked Data

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The Linked Data Cube Vocabulary

http://inspector.sindice.com/inspect?url=http://reference.data.gov.uk/def/payment

http://inspector.sindice.com/inspect?url=http://purl.org/linked-data/cube&content=




UK government: Top-down approach to

standardization for Spending Data

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Statistical Data perspective

Linked Data Cube Vocabolary

Payment Ontology

Live example index







Enrollment number for a study

from ClinicalTrial.gov

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Semantic Web Health Care

and Life Sciences (HCLS)

Interest Group


(Life Science part of the

Linking Open Data cloud)

2



Enrollment number for a study

from ClinicalTrial.gov

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2 of 48 Triples


2



Interest Group


(Life Science part of the

Linking Open Data cloud)

http://inspector.sindice.com/inspect?url=http://data.linkedct.org/resource/trials/NCT00755378&content=



An example of first using the source data

structure as the ”standard” …

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2 of 48 Triples


2

Database key Variabel name Table name

http://inspector.sindice.com/inspect?url=http://data.linkedct.org/resource/trials/NCT00755378&content=



… and then as a next step look for a

common standard

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Interest Group

Translational Medicine Ontology

(a.k.a. Pharma Ontology)

Live example index

http://inspector.sindice.com/inspect?url=http://www.w3.org/2001/sw/hcls/ns/transmed&content=



Population of Brussels Capital

Region from Wikipedia

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3

http://inspector.sindice.com/inspect?url=http://dbpedia.org/page/Brussels&content=



Linking between different sources about

the same entity using different identifiers


3

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http://inspector.sindice.com/inspect?url=http://dbpedia.org/page/Brussels&content=



Bottom-up standardization: Community

curated, and a central shallow Ontology

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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

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Linked Open Data star scheme

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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

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http://www.agfa.com/w3c/2009/drugAdministrationForms#

http://linkedlifedata.com/resource/umls/id/C1879952


• EU Project – LarKC

• Published CDISC CT:s as part of Linked Life Data





Pragmatic first steps, start with

Trial Summary Parameters

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Existing text strings published in a long file in Excel txt format (soon also as ODM/XML) 0





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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

Establish a CDISC URI scheme

Proposal: Build on http://data.gov.uk/resources/uris 1

Model CDISC SDTM CT:s as RDF Triples 2

http://data.gov.uk/resources/uris





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Establish a CDISC URI scheme

Proposal: Build on http://data.gov.uk/resources/uris 1

Model CDISC SDTM CT:s as RDF Triples 2

Publish in RDF/XML 3

Create a so called SPARQL endpoint so that CDISC

standards published as triples can be queried

directly using the RDF query language.

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De-reference/look-up service so people

and applications can get descriptions of

individual code lists and code.

4

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




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

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Internal

categorization to

support Design &

Interpretation

decisions

A scenario:

Linked Clinical Study Metadata

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http://clinial.data.astrazeneca.com/id/study/D8180C00011

http://data.linkedct.org/resource/trials/NCT00755378

What would we like to see as the

linked data description of it?

What would we like to see on a

internal webpage

presenting linked data

describing a clinical study?

owl:sameAs

More ideas



Explore the use of BRIDG and TMO

for common classes and properties

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Interest Group

Translational Medicine Ontology




Linking Clinical Data: Explore URI

scheme and minting URI:s

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Proposal: Build on http://data.gov.uk/resources/uris




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

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If you want to learn more

42

An Intro To The Semantic Web: Why You Need To

Know About It Sooner Than Later , by Samantha Wong

Image Source: Frederic Martin

The Semantic Web 2010 Status Update

by Prof .Jim Hendler

Open data: accountability, citizen utility

and economic opportunity.

http://data.gov.uk/linked-data

http://www.data.gov/semantic

Linked Spending Data –

How and Why Bother


Interest Group for Semantic Web in

Health Care and Life Science

http://www.w3.org/blog/hcls

Linked Open Data star scheme by example

The Linking Open Data

cloud diagram

Guide to the

Payments Ontology

The RDF Data Cube

vocabulary

Presentation:

Statistical Data in RDF

How DBpedia Treats

Wikipedia as a Database

Excellent article “More than Words: Biomedical Ontologies”

http://www.webcentralstation.ca/2011/02/08/an-intro-to-the-semantic-web-why-you-need-to-know-about-it-sooner-than-later/

http://www.webcentralstation.ca/2011/02/08/an-intro-to-the-semantic-web-why-you-need-to-know-about-it-sooner-than-later/

http://fredericmartin.typepad.com/myblog/2007/11/from-web10-to-w.html

http://www.slideshare.net/jahendler/the-semantic-web-2010-update-5673441


http://gov20.govfresh.com/open-data-accountability-citizen-utility-and-economic-opportunity/






http://www.data.gov/semantic

http://blogs.talis.com/nodalities/2011/01/linked-spending-data-how-and-why-bother-pt1.php





http://www.w3.org/wiki/HCLSIG/LODD

http://www.w3.org/blog/hcls

http://lab.linkeddata.deri.ie/2010/star-scheme-by-example/

http://richard.cyganiak.de/2007/10/lod/



http://data.gov.uk/resources/payments



http://inspector.sindice.com/inspect?url=http://spending.lichfielddc.gov.uk/spend/8605670&content=

http://publishing-statistical-data.googlecode.com/svn/trunk/specs/src/main/html/cube.html



http://www.slideshare.net/jindrichmynarz/statistical-data-in-rdf

http://www.readwriteweb.com/cloud/2011/01/how-dbpedia-treats-wikipedia-a.php





http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2011_02_11/caredit.a1100012



And now – An Evening with TinTin

at the Brussels Comic Strip Center!

43

Technology

Linking clinical data standards