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.
(RIYA)🎄Airhostess Call Girl Jaipur Call Now 8445551418 Premium Collection Of ...
AMIA 2019: Unleashing the value of CDEs through CEDAR
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. Disclosure
I and my spouse/partner have no relevant relationships with
commercial interests to disclose.
2AMIA 2019 | amia.org
3. 3AMIA 2019 | amia.org
What is this colored picture about?
5. [Your presentation on this and next slides]
5AMIA 2017 | amia.org
Metadata authoring is hard
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. 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
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
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. 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. 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. NCI uses “common data elements” as
metadata for fields in CRFs
14AMIA 2019 | amia.org
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. 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. 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. 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
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. Representing CDEs in CEDAR will allow authoring of
CEDAR templates that can provide the basis for eCRFs
Template FieldCase Report Form
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
CEDAR works with CDEs in two different ways. The first is as a repository of information, comparable to the CDE browser.
High-level overview of the workflow of ingesting libraries of CDEs into CEDAR. CDEs from an external library are transformed to the CEDAR model and uploaded to the CEDAR Workbench via the CEDAR REST APIs. The controlled term value sets used by these CDEs are stored in BioPortal. The biomedical community can easily access and reuse the CDEs when building Web-based metadata acquisition forms. The CDEs can also be accessed via the CEDAR REST APIs.
What we just described could be considered the CRF Repository mode.
And it only gets confusing because CEDAR uses the same tool to represent both CRFs and CDEs.
In the future, we could make adjustments to CEDAR to distinguish those two modes.
