“Pushing Back”
Standards and
Standard Organizations
in a Semantic Web Enabled World
Kerstin Forsberg
Informatics Scientist...
Purpose
Encourage standard organisations to
“Use Standards for Standards”

Agenda
• Standards for Data and Semantics
• Exe...
Kerstin Forsberg (@kerfors)
“Information architect, semantic web and linked data enthusiast
caring about clinical trial da...
About AstraZeneca

• Alongside our own R&D, we partner
with others, combining skills and
resources to broaden the potentia...
AstraZeneca’s view on “Semantics”
Enabling the hyperconnected enterprise
“We need to build a linked
data architecture enab...
Standards for Data and Semantics
Different types of standards
• Entity-based Ontologies
• Concept-based Terminologies/Code...
Standards for Data and Semantics
Examples
• Entity-based Ontologies
• Concept-based Terminologies/Code systems

• Code lis...
“Pushing back” – Use standards for standards
1. NCI (National Cancer Institute)Thesaurus
• Entity-based Ontologies
• Conce...
“Pushing back” – Use standards for standards
AZ Vocabulary Management team shared this with NCI EVS

• The NCI Thesaurus i...
“Pushing back” – Use standards for standards
2. MedDRA (Medical Dictionary for Regulatory Activities)
• Entity-based Ontol...
“Pushing back” – Use standards for standards
AZ Vocabulary Management team shared this with MedDRA MSSO
A very simple SKOS...
“Pushing back” – Use standards for standards
3. CDISC (Clinical Data Interchange Consortium)
• Entity-based Ontologies
• C...
Standards for Data Exchange
Clinical Trial Data standardized “containers”

Patient level
Submission standards SDTM
“design...
Standards for Data Exchange
Documentation of standardized “containers”

Human readable
documentation in 200+
pages PDF:s, ...
Standards for Data Exchange
Data in standardized “containers”

CDISC SDTM
Implementation
Guideline (IG)

Humans can connec...
Standards for Data Exchange
Documentation of Standard fragments
CDISC SDTM
Model

1

2

CDISC SDTM
Implementation
Guidelin...
Standards for Data Exchange
Linked Clinical Data Standards
• CDISC2RDF started as a cross-pharma precompetitive project wi...
Standards for Data Exchange
Linked Clinical Data Standards

Human readable documentation in
PDF:s, Excel:s (and some in XM...
Standards for Data Exchange
Linked Clinical Data Standards
Meta Model Schema (mms)
Based on the core ISO11179 model
(metad...
Standards for Data Exchange
Annotating existing standards
Meta Model Schema (mms)
Based on the core ISO11179 model
(metada...
CDISC and NCIT
Value sets is an issue

• Concept-based Terminologies / Code systems

• Code lists/Value sets/Term sets
mms...
Standards for Data Exchange
Cross standard review and mappings

Data Elements [SDTM, ADaM, CDASH] ”haveSame” Value Domain ...
Provenance/Justification for Mappings
Example from EU project SALUS for Post Market Safety Studies

The example show the h...
Provenance/Justification for Mappings
Example from EU project SALUS for Post Market Safety Studies

MedDRA:10028596

skos:...
Provenance/Justification for Mappings
Alternative: Mappings as LinkSets

The Dataset Descriptions for the Open
Pharmacolog...
Provenance/Justification for Mappings
Alternative: Mappings as Nanopublications

MedDRA:10028596

26

Kerstin Forsberg | S...
Summary
Encourage standard organisations to
“Use Standards for Standards”
for sustainability and trustability.
Think if …
...
Acknowledgements
AZ’s Semantic Web Community of Practice members:
Tom Plasterer (lead), Jim Morris, Courtland Yockey, Sora...
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Pushing back, standards and standard organizations in a Semantic Web enabled world

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Keynote at SWAT4LS (Semantic Web Applications and Tools for Life Science) 2013

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Pushing back, standards and standard organizations in a Semantic Web enabled world

  1. 1. “Pushing Back” Standards and Standard Organizations in a Semantic Web Enabled World Kerstin Forsberg Informatics Scientist AstraZeneca Mölndal, Sweden Image: Flickr bitpuddle (Twitter @eric_d_hancock)
  2. 2. Purpose Encourage standard organisations to “Use Standards for Standards” Agenda • Standards for Data and Semantics • Exemplas of Standard Organizations now looking into using Semantic Web • Provenance/Justification for Mappings 2 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  3. 3. Kerstin Forsberg (@kerfors) “Information architect, semantic web and linked data enthusiast caring about clinical trial data.” • “Volvo Web Wave Project” 1995-1997 W3C conferences 1996 & 1999, Dublin Core, RDF • “Extensible use of RDF in a business context” paper presented at the W3C WWW9 conference, 2000, Amsterdam • “Advancing translational research with the Semantic Web” joint W3C HCLS paper in BMC Bioinformatics, 2007 • “Linked data, an opportunity to mitigate complexity in pharmaceutical research and development” Summary of experiences from LarKC and W3C HCLS 2011 together with my colleague Bosse Andersson 3 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  4. 4. About AstraZeneca • Alongside our own R&D, we partner with others, combining skills and resources to broaden the potential for successful innovation. • We believe that only by working together with others who have a part of play in improving healthcare can real progress be made. • We work closely with others in the healthcare community, including physicians and those who pay for healthcare, to understand their challenges and how we can combine skills and resources to achieve a common goal: improved health. 4 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  5. 5. AstraZeneca’s view on “Semantics” Enabling the hyperconnected enterprise “We need to build a linked data architecture enabling us to ask questions and solve business problems across a heterogeneous information landscape extending beyond the traditional boundaries of the enterprise.” semanticsconnectsusall 5 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  6. 6. Standards for Data and Semantics Different types of standards • Entity-based Ontologies • Concept-based Terminologies/Code systems • Code lists/Value sets/Term sets • Data exchange (Tabulated data) • Information Models 6 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  7. 7. Standards for Data and Semantics Examples • Entity-based Ontologies • Concept-based Terminologies/Code systems • Code lists/Value sets/Term sets • Data exchange (Tabulated data) • Information Models 7 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  8. 8. “Pushing back” – Use standards for standards 1. NCI (National Cancer Institute)Thesaurus • Entity-based Ontologies • Concept-based Terminologies/Code systems • Code lists/Value sets/Term sets • Data exchange (Tabulated data) • Information Models 8 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  9. 9. “Pushing back” – Use standards for standards AZ Vocabulary Management team shared this with NCI EVS • The NCI Thesaurus is an extensive medical vocabulary published by the US National Institutes of Health: http://ncit.nci.nih.gov/ • It is made available in several downloadable formats: http://evs.nci.nih.gov/ftp1/NCI_Thesaurus • In order for use to use the thesaurus in our system, we need to convert it to RDF, following the SKOS standard: http://www.w3.org/2004/02/skos/ Jim Morris, Informatics Scientist AstraZeneca R&D Wilmington, USA 9 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  10. 10. “Pushing back” – Use standards for standards 2. MedDRA (Medical Dictionary for Regulatory Activities) • Entity-based Ontologies • Concept-based Terminologies/Code systems • Code lists/Value sets/Term sets • Data exchange (Tabulated data) • Information Models 10 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  11. 11. “Pushing back” – Use standards for standards AZ Vocabulary Management team shared this with MedDRA MSSO 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) 11 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 Courtland Yockey, Informatics Scientist AstraZeneca R&D Wilmington, USA AZIT | R&D Information
  12. 12. “Pushing back” – Use standards for standards 3. CDISC (Clinical Data Interchange Consortium) • Entity-based Ontologies • Concept-based Terminologies / Code systems • Code lists/Value sets/Term sets • Data exchange (Tabulated data) • Information Models 12 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  13. 13. Standards for Data Exchange Clinical Trial Data standardized “containers” Patient level Submission standards SDTM “designed so [FDA] reviewers with no tools other than perhaps the SAS Viewer would be able to open a dataset and browse it easily”. 13 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 Trial Summary level AZIT | R&D Information
  14. 14. Standards for Data Exchange Documentation of standardized “containers” Human readable documentation in 200+ pages PDF:s, Excel:s (and some in XML). 14 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  15. 15. Standards for Data Exchange Data in standardized “containers” CDISC SDTM Implementation Guideline (IG) Humans can connect data to data standards. 15 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  16. 16. Standards for Data Exchange Documentation of Standard fragments CDISC SDTM Model 1 2 CDISC SDTM Implementation Guideline (IG) 3 CDISC SDTM Humans can connect data to data standards and connect the different standard fragments to each other. 16 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 Controlled Terminiolgy AZIT | R&D Information
  17. 17. Standards for Data Exchange Linked Clinical Data Standards • CDISC2RDF started as a cross-pharma precompetitive project with AstraZeneca, Roche, W3C et al. to show case Semantic Web standards and Linked Data principles. • Become part of the Semantic Technology project, a FDA/PhUSE working group for Emerging Technologies, with 30+ repr. from FDA, CDISC, Pharma:s, CRO:s and software vendors. • First phase: Representing existing “container” standards (SDTM, CDASH, SEND, ADaM) in RDF. 17 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  18. 18. Standards for Data Exchange Linked Clinical Data Standards Human readable documentation in PDF:s, Excel:s (and some in XML) Machine processable linked data structured as RDF triples (160.000+ ) Serializations of RDF triples in Turtle and XML … https://github.com/phuse-org/rdf.cdisc.org 18 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  19. 19. Standards for Data Exchange Linked Clinical Data Standards Meta Model Schema (mms) Based on the core ISO11179 model (metadata for data elements and a few CDISC specific classes and properties) Import files Human readable documentation in Annotated Excel files from CDISC with classes and properties from the Schemas PDF:s, Excel:s (and some in XML) ready to transform to RDF triples using a off-the-shelf tool (TopQuadrant Composer) Machine processable linked data structured as RDF triples (160.000+ ) Serializations of RDF triples in Turtle and XML … https://github.com/phuse-org/rdf.cdisc.org 19 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  20. 20. Standards for Data Exchange Annotating existing standards Meta Model Schema (mms) Based on the core ISO11179 model (metadata for data elements and a few CDISC specific classes and properties) This turned out to be a good way to communicate with people knowledgeable in CDISC but new to RDF schemas to understand the process of “triplification”. 20 Import files Annotated Excel files from CDISC with classes and properties from the Schemas ready to transform to RDF triples using a off-the-shelf tool (TopQuadrant Composer) Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  21. 21. CDISC and NCIT Value sets is an issue • Concept-based Terminologies / Code systems • Code lists/Value sets/Term sets mms:PermissibleValue mms:ValueDomain • Data exchange (Tabulated data) mms:Data Element mms:Dataset mms:DataCollectionForm 21 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  22. 22. Standards for Data Exchange Cross standard review and mappings Data Elements [SDTM, ADaM, CDASH] ”haveSame” Value Domain (CT) 22 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  23. 23. Provenance/Justification for Mappings Example from EU project SALUS for Post Market Safety Studies The example show the hierarchy of cardiac disorders in both the MedDRA and SNOMED-CT concept schemes, expressed using the skos:broader property. Mappings between similar concepts in both concept schemes are stated using the skos:exactMatch property. From: SALUS Harmonized Ontology for Post Market Safety Studies 23 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  24. 24. Provenance/Justification for Mappings Example from EU project SALUS for Post Market Safety Studies MedDRA:10028596 skos:exactMatch SNOMEDCT:22298006 The example show the hierarchy of cardiac disorders in both the MedDRA and SNOMED-CT concept schemes, expressed using the skos:broader property. Mappings between similar concepts in both concept schemes are stated using the skos:exactMatch property. From: SALUS Harmonized Ontology for Post Market Safety Studies 24 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  25. 25. Provenance/Justification for Mappings Alternative: Mappings as LinkSets The Dataset Descriptions for the Open Pharmacological Space is a specification for the metadata to described datasets, and the LinkSets that relate them. 25 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  26. 26. Provenance/Justification for Mappings Alternative: Mappings as Nanopublications MedDRA:10028596 26 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 skos:exactMatch SNOMEDCT:22298006 AZIT | R&D Information
  27. 27. Summary Encourage standard organisations to “Use Standards for Standards” for sustainability and trustability. Think if … semanticsconnectsusall 27 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information
  28. 28. Acknowledgements AZ’s Semantic Web Community of Practice members: Tom Plasterer (lead), Jim Morris, Courtland Yockey, Sorana Popa, Rob Hernandez, Mike Westaway, Rajan Desai, Simon Rakov, Dana Crowley, Ian Dix, Johan Törnqvist Collaborators and Advisors: • Charlie Mead – IO Informatics • Dean Allemang – Working Ontologist • Frederik Malfait – IMOS consulting / Roche • Phil Ashworth – TopQuadrant Thank you! Kerstin.l.forsberg@astrazeneca.com 28 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information

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