CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata

1. CEDAR is powered by BioPortal, the world’s
most comprehensives repository of
biomedical and earth science ontologies, to
provide controlled terms for metadata.
CEDAR: Web-Based Tools for Accelerating the Creation of Standardized Metadata
Mark A. Musen1
, John Graybeal1
, Martin J. O'Connor1
, Marcos Martínez-Romero1
, Attila L. Egyedi1
, Debra Willrett1
, S. Ahmad Chan Bukhari2
,
Steven H. Kleinstein2
, Kei-Hoi Cheung2
, Elizabeth Thomson3
, Alejandra Gonzalez-Beltran4
, Phillipe Rocca-Serra4
, and Susanna-Assunta Sansone4
1
Stanford University; 2
Yale University; 3
Northrop Grumman, Inc.; 4
Oxford University
https://metadatacenter.org
(4) SUBMIT METADATA(3) FILL IN METADATA(2) DESIGN TEMPLATE
Template Designer Metadata Editor
Template authors Metadata authors
Metadata Repositorytemplate metadata
LINCS
Public Databases
https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/ab105771-564e-42a1-9be4-5a63891… https://cedar.metadatacenter.org/instances/edit/https://repo.metadatacenter.org/template-instances/d4f1059e-8e27-4166-902f-…
A sample study
Acute stress disorder
Stanford University
John Doe
Longitudinal
(1) EXPLORE METADATA
Resource Manager
Template authors / Scientists
https://cedar.metadatacenter.org/dashboard?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2F232ab017-ec1e-4…
search, browse, and share metadata
create
templates
create
metadata
cedar.metadatacenter.org
CEDAR lets users create complete and comprehensive metadata for any
scientific domain using standard ontologies and data structures.
VALIDATE and PUBLISHTEMPLATES METADATAWORKSPACE
Building templates involves composing forms
of fields, each with a name and description.
Templates
CEDAR provides you a workspace to store
your templates, elements and metadata.
Organize your project into folders and
manage your metadata over time..
Folders
JSON-LD
Create, read, update and delete with CEDAR
REST API microservices. Send metadata to
your repository or app, or publish to CEDAR!
REST APIs
DELETE /folders/{id}
GET /folders/{id}
GET /folders/{id}/details
POST /folders
Collaborate with your team using groups.
Share documents and folders in CEDAR with
your team members. Publish your templates
to the community by making them public.
Share
Adoption and Evaluation
“organism”: {
“@type”: “http://data.bioontology.org/
ontologies/NCBITAXON/classes/
http%3A%2F%2Fpurl.bioontology.org%2
Fontology2FSTY%2FT001”,
“@id”:”http://purl.obolibrary.org/
NCBITAXON/9606” }
Templates and metadata are represented as
JSON-LD, a machine-readable and widely
accepted interchange format on the Web.
Basic field types include short and long text,
numbers, email, and more.
Sample Name
Enter Field Title
Enter the name of your sample.
Enter Field Description
Elements are reusable groups of fields and
other elements. Elements can be shared on
CEDAR and nested to any level. Using
elements enables templates to be composed
of community-defined building blocks to meet
common specifications or needs.
Elements
CEDAR supports features that allow easy
and rapid entry of metadata. Computer-
assisted intelligent authoring provides
suggestions for both fields and values.
Metadata
Organism
Amphibian
OK
BioSample Human
Sample Name
Animal
Archaeon
a |
Isolate
Age
Biomaterial Provider
Tissue
Sex
~ 700
scientific
ontologies
CEDAR is supported by grant U54 AI117925 awarded by the National Institute of Allergy and Infectious Diseases through funds provided by the trans-NIH Big Data to Knowledge (BD2K) initiative (www.bd2k.nih.gov).
Automatic validation is done on the fly to give
immediate feedback of errors. The validator
framework wraps other existing validation
services, e.g., the BioSample Validator.
Validation
03/2018