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AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 1 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 2 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 3 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 4 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 5 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 6 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 7 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 8 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 9 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 10 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 11 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 12 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 13 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 14 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 15 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 16 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 17 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 18 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 19 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 20 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 21 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 22 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 23 AMIA 2019: Unleashing the value of CDEs through CEDAR Slide 24
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AMIA 2019: Unleashing the value of CDEs through CEDAR

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With the CEDAR system users build templates for easily collecting rich metadata. Questions that have been defined as Common Data Elements in the National Cancer Institute's caDSR have been imported as CEDAR fields, for re-use by CEDAR's template builders.

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AMIA 2019: Unleashing the value of CDEs through CEDAR

  1. 1. Mark A. Musen1 Author list: Martin J. O’Connor1, Denise B. Warzel2, Marcos Martínez-Romero1, Josef Hardi1, Debra Willrett1, Attila L. Egyedi1, Aras Eftekhari3, John Graybeal1, Mark A. Musen1 1Stanford University; 2National Cancer Institute; 3Attain LLC Unleashing the value of Common Data Elements through the CEDAR Workbench Translating Text and Ontologies S70
  2. 2. Disclosure I and my spouse/partner have no relevant relationships with commercial interests to disclose. 2AMIA 2019 | amia.org
  3. 3. 3AMIA 2019 | amia.org What is this colored picture about?
  4. 4. 4AMIA 2017 | amia.org
  5. 5. [Your presentation on this and next slides] 5AMIA 2017 | amia.org Metadata authoring is hard
  6. 6. 6AMIA 2017 | amia.org An analysis of metadata from NCBI’s BioSample • 73% of “Boolean” values • nonsmoker, former-smoker • 26% of “integer” values • JM52, UVPgt59.4, pig • 68% of ontology terms • presumed normal, wild_type Gonçalves, R. S., & Musen, M. A. (2019). The variable quality of metadata about biological samples used in biomedical experiments. Scientific Data, 6, 190021. https://doi.org/10.1038/sdata.2019.21 Poor metadata
  7. 7. FAIR Principles to enhance the value of digital resources and their metadata 7AMIA 2019 | amia.org Findable, Accessible, Interoperable, Reusable https://www.nature.com/articles/sdata201618
  8. 8. The CEDAR approach to metadata 8AMIA 2019 | amia.org
  9. 9. 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 9AMIA 2019 | amia.org
  10. 10. 10AMIA 2019 | amia.org
  11. 11. 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 11AMIA 2019 | amia.org
  12. 12. CEDAR takes 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 12AMIA 2019 | amia.org THE NATIONALCENTER FOR BIOMEDICAL ONTOLOGY
  13. 13. But there are different kinds of specifications! Templates describing classes of experiments Ontologies describing potential values Metadata (CDEs) describing reusable question specifications for collecting and reporting data 13AMIA 2019 | amia.org
  14. 14. NCI uses “common data elements” as metadata for fields in CRFs 14AMIA 2019 | amia.org
  15. 15. ISO/IEC 11179 • International standard for representing metadata • Provides: • Guidelines for the naming and definition of data elements • Information about the metadata that must be captured for data elements • Rules for the way data elements are created and registered 15AMIA 2019 | amia.org
  16. 16. NCI’s Cancer Data Standards Repository (caDSR) • One of the largest CDE registries (over 60,000 CDEs) • Based on ISO/IEC 11179 16AMIA 2019 | amia.org
  17. 17. Bringing CDEs to the masses • Practical challenges to reusing CDEs limit their adoption by the biomedical community • ISO/IEC 11179 does not specify implementation-level details • Complex ISO conformance requirements • We extended the CEDAR Workbench to support CDEs • We incorporated over 49K caDSR CDEs into CEDAR • These CDEs are publicly available on CEDAR 17AMIA 2019 | amia.org
  18. 18. We developed a CDE ingestion workflow 18AMIA 2019 | amia.org CEDAR Repository Metadata Creator Metadata Editor https://cedar.metadatacenter.org/instances/edit/https://repo.me tadatacenter.org/template-instance s/d4f1059e-8e27-4166-902f-… A sample study Acute str ess disor der Stanfor d University John Doe Longitudinal Resource Manager https://cedar.me tadatacenter.org/dashboard?folderId=https:%2F%2Frepo.me tadatacenter.org%2Ffolders%2F232ab017-e c1e-4… Template Designer https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/ab105771-564e-42a1-9be4-5a63891… CEDAR Open Services CEDAR CDEs CEDAR Fields CEDAR Templates Semantic Web Standards CDE Library CEDAR Workbench Transformation and Ingestion BioPortal Ontology Repository Biomedical Community 49,280 caDSR CDEs 8,808 value sets 114,121 values
  19. 19. 19AMIA 2019 | amia.org
  20. 20. 20AMIA 2019 | amia.org
  21. 21. What CDEs Bring CEDAR Template slots for experimental metadata … • Can still refer to ontologies and value sets as the source of values for data items • Are able to refer to CDEs as the source of values or datatype restrictions for data items CEDAR is able to interoperate with both kinds of standards
  22. 22. Representing CDEs in CEDAR will allow authoring of CEDAR templates that can provide the basis for eCRFs Template FieldCase Report Form
  23. 23. Summary • We extended CEDAR to natively support CDEs • We ingested a library of over 49K CDEs and associated value sets • These CDEs are publicly available for general use on CEDAR • Users can create templates using CDE-based fields • Users can create FAIR metadata → Enhanced data Findability 23AMIA 2019 | amia.org
  24. 24. Thank you! Email me at: musen@Stanford.EDU https://metadatacenter.org

With the CEDAR system users build templates for easily collecting rich metadata. Questions that have been defined as Common Data Elements in the National Cancer Institute's caDSR have been imported as CEDAR fields, for re-use by CEDAR's template builders.

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