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

“Pushing Back”Standards and Standard Organizations in a Semantic Web Enabled World

Kerstin ForsbergInformatics ScientistAstraZenecaMölndal, Sweden

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AZIT | R&D Information

Purpose

Encourage standard organisations to“Use Standards for Standards”

Agenda

• Standards for Data and Semantics

• Exemplas of Standard Organizationsnow looking into using Semantic Web

• Provenance/Justification for Mappings

2 Kerstin Forsberg | SWAT4LS, Dec 10th 2013


Kerstin Forsberg (@kerfors)

• “Volvo Web Wave Project” 1995-1997W3C 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 HCLS2011 together with my colleague Bosse Andersson

“Information architect, semantic web and linked data enthusiast caring about clinical trial data.”



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.


AstraZeneca’s view on “Semantics”

Enabling the hyperconnected enterprise

5 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D Information

“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

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

Standards for Data and Semantics

Examples







“Pushing back” – Use standards for standards

1. NCI (National Cancer Institute)Thesaurus







“Pushing back” – Use standards for standardsAZ 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 ScientistAstraZeneca R&D Wilmington, USA

http://ncit.nci.nih.gov/

http://evs.nci.nih.gov/ftp1/NCI_Thesaurus

http://www.w3.org/2004/02/skos/

“Pushing back” – Use standards for standards2. MedDRA (Medical Dictionary for Regulatory Activities)







“Pushing back” – Use standards for standardsAZ Vocabulary Management team shared this with MedDRA MSSO

11 Kerstin Forsberg | SWAT4LS, Dec 10th 2013 AZIT | R&D InformationCourtland Yockey, Informatics ScientistAstraZeneca R&D Wilmington, 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)

“Pushing back” – Use standards for standards

3. CDISC (Clinical Data Interchange Consortium)



• Concept-based Terminologies / Code systems




Standards for Data Exchange

Clinical Trial Data standardized “containers”


Trial Summary level

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”.


Documentation of standardized “containers”


Human readable documentation in 200+ pages PDF:s, Excel:s (and some in XML).


Data in standardized “containers”


CDISC SDTMImplementationGuideline (IG)

Humans can connect data to data standards.


Documentation of Standard fragments


CDISC SDTM Model 1

CDISC SDTMImplementationGuideline (IG)

2

CDISC SDTMControlled Terminiolgy

3Humans can connect data to data standards and connect the different standard fragments to each other.


Linked Clinical Data Standards


• CDISC2RDF started as a cross-pharma pre-competitive 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.

http://cdisc2rdf.com/

http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology




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 triplesin Turtle and XML …

https://github.com/phuse-org/rdf.cdisc.org





Human readable documentation in PDF:s, Excel:s (and some in XML)

Import filesAnnotated 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)

Meta Model Schema (mms)Based on the core ISO11179 model

(metadata for data elements and a few CDISC specific classes and properties)

Machine processable linked data structured as RDF triples(160.000+ )


Serializations of RDF triplesin Turtle and XML …



Annotating existing standards


Import filesAnnotated 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)

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”.

CDISC and NCIT

Value sets is an issue


• Concept-based Terminologies / Code systems



mms:PermissibleValue

mms:ValueDomain

mms:Datasetmms:Data Element

mms:DataCollectionForm


Cross standard review and mappings


Data Elements [SDTM, ADaM, CDASH] ”haveSame” Value Domain (CT)

Provenance/Justification for MappingsExample from EU project SALUS for Post Market Safety Studies


The example show the hierarchy of cardiac disorders in both the MedDRA andSNOMED-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

http://www.srdc.com.tr/projects/salus/docs/SALUS_D4.3.1%20Harmonized%20Ontology%20for%20Post%20Market%20Safety%20Studies%20%E2%80%93R1%20v1.0_FINAL.pdf

Provenance/Justification for MappingsExample from EU project SALUS for Post Market Safety Studies


The example show the hierarchy of cardiac disorders in both the MedDRA andSNOMED-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

MedDRA:10028596 skos:exactMatch SNOMEDCT:22298006

http://www.srdc.com.tr/projects/salus/docs/SALUS_D4.3.1%20Harmonized%20Ontology%20for%20Post%20Market%20Safety%20Studies%20%E2%80%93R1%20v1.0_FINAL.pdf

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.

http://www.openphacts.org/specs/2013/WD-datadesc-20130912/

http://www.openphacts.org/specs/2013/WD-datadesc-20130912/

Provenance/Justification for Mappings

Alternative: Mappings as Nanopublications


MedDRA:10028596 skos:exactMatch SNOMEDCT:22298006


Summary

Encourage standard organisations to“Use Standards for Standards”

for sustainability and trustability.

Think if …


semanticsconnectsusall


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! [email protected]

mailto:[email protected]

Education

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