Use of Standard Common Data Elements (CDEs) in CEDAR...Use of Standard Common Data Elements (CDEs) in CEDAR Mark A. Musen, M.D., Ph.D. Kathryn Collins Martin O’Connor, M.S. John

Use of Standard Common Data Elements (CDEs) in CEDAR

Mark A. Musen, M.D., Ph.D.Kathryn Collins

Martin O’Connor, M.S.John Graybeal

Stanford Center for Biomedical Informatics ResearchDepartment of Medicine

Stanford University School of [email protected]

The CEDAR Approach to Metadata

The CEDAR Approach to Standards

• Operating on Big Data requires all kinds of standards

• We don’t want to be in the standards business ourselves

• We want to be able to accommodate the standards that come from the biomedical community

• We need an adaptable infrastructure where standard specifications are themselves editable

Some key features of CEDAR• All semantic components—template elements,

templates, ontologies, and value sets—are managed as first-class entities

• User interfaces and drop-down menus are not hardcoded, but are generated on the fly from CEDAR’s semantic content

• All software components have well defined APIs, facilitating reuse of software by a variety of clients

• CEDAR generates all metadata in JSON-LD, a widely adopted Web standard that can be translated into other representations

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CEDAR was designed to take advantage of ontology standards

• Standard templates derived from community-based minimal information models

• Templates rendered as frames that can be instantiated with standard values

• Template slots filled using standard ontologies and value sets

THE NATIONAL CENTER FORBIOMEDICAL ONTOLOGY

But there are different kinds of metadata specifications!

• Templates describing classes of experiments—

• Ontologies describing potential values

• Metadata (CDEs) describing data types and value sets —

NCI uses “common data elements” as metadata for fields in CRFs

CDEs are based on ISO/IEC 11179 model

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Describing CDEs in CEDAR

Data Element model

represented as

CEDAR Template

Common Data Element Template

CDE Instance

represented as

CEDAR Metadata Instance

Access Route of Administration Text Code

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Representing CDEs in CEDAR will allow authoring of CEDAR templates that can

provide the basis for eCRFs

Case Report Form 3517797: New Primary Cancer

Template

What CDEs Will Bring CEDAR

• Template slots for experimental metadata …– Can still refer to ontologies and value sets as the

source of values for data items– Will also be able to refer to CDEs as the source of

values or datatype restrictions for data items

• CEDAR will be able to interoperate with both kinds of standards

CEDAR Accommodates Many Kinds of Standards

• Templates for Describing Biomedical Experiments

• Ontologies for providing values• CDEs for providing values• APIs for accessing software components

And CEDAR makes all these specifications editable!

The CEDAR Approach to Standards

• Operating on Big Data requires all kinds of standards

• We don’t want to be in the standards business ourselves

• We want to be able to accommodate the standards that come from the biomedical community

• We need an adaptable infrastructure where standard specifications are themselves editable

http://metadatacenter.org

Use of Standard Common Data Elements (CDEs) in CEDAR�The CEDAR Approach to MetadataThe CEDAR Approach to StandardsSlide Number 4Slide Number 5Slide Number 6Some key features of CEDARCEDAR was designed to take advantage of ontology standardsSlide Number 9Slide Number 10But there are different kinds of metadata specifications!NCI uses “common data elements” as metadata for fields in CRFsCDEs are based on ISO/IEC 11179 modelSlide Number 14Describing CDEs in CEDARSlide Number 16Representing CDEs in CEDAR will allow authoring of CEDAR templates that can provide the basis for eCRFsWhat CDEs Will Bring CEDARCEDAR Accommodates Many Kinds of StandardsThe CEDAR Approach to StandardsSlide Number 21