Finding and Reusing Biomedical Datasets using CEDAR Metadata Repository and Tools

1. Finding and Reusing Biomedical Datasets using CEDAR Metadata
Repository and Tools
CEDAR is making data submission smarter and faster, so that biomedical researchers and analysts can create and use better metadata.
Through better interfaces, terminology, metadata practices, and analytics, CEDAR optimizes the metadata pathway from provider to end user.
CEDAR
CENTER FOR EXPANDED DATA
ANNOTATION AND RETRIEVAL
CEDAR
R FOR EXPANDED DATA
ATION AND RETRIEVAL
metadatacenter.org
, John Campbell 2, Jeff Wiser 2 , Kim A. Durante 1 , Alejandra Gonzalez-Beltran 4 , Philippe Rocca-Serra 4 , Susanna-Assunta Sansone 4Steven H. Kleinstein 3 , Mark A. Musen 1
, Kei-Hoi Cheung 3, Attila L. Egyedi 1 , John Graybeal 1, Purvesh Khatri 1, Ravi D. Shankar 1Martin J. O'Connor 1, , Olivier Gevaert 1, Marcos Martinez-Romero 11Debra Willrett , Syed Ahmad Chan Bukhari 3
2
Northrop Grumman, Inc.; 3Yale University; 4Oxford UniversityStanford University;1
5/2017CEDAR 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).
TEMPLATES
Create, read, update, and delete using the
CEDAR REST API. Export templates and
metadata to your repository or application.
Go to metadatacenter.org/tools-training/
cedar-api for the complete list.
CEDAR API
DELETE /folders/{id}
GET /folders/{id}
GET /folders/{id}/details
POST /folders
PUT /folders/{id}
PUT /folders/{id}/permissions
Building templates involves composing
forms of fields, each with a name and
description.
Templates
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
Date
Ǜ Email
# Number
Phone
- - Break
Video
Image
Element
WORKSPACE
CEDAR gives you a workspace to store
your template and metadata resources.
Organize your projects using folders, and
manage your metadata over multiple
submissions.
Folders
BioSample Templates
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. Create reusable elements and share
them with the community or your team.
Share
My Team
Create a group
+
Search for resources shared with you or in
your workspace. Filter results by resource
type.
Search
Filter by Type
METADATA
CEDAR has a submission service for
submitting data directly to NCBI repositories
such as BioSample, BioProject, and SRA.
This provides an end-to-end solution for
metadata creation and submission of
biomedical data.
NCBI Submission
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
RESOURCES
Check out CEDAR on Twitter and
Facebook. Go to metadatacenter.org/
community/engagement
Engagement
CEDAR is powered by BioPortal, the world’s
most comprehensive repostory of
biomedical ontologies, to provide controlled
terms for metadata.
Ontology: NCBITAXON
Viroids
Viruses
Other Sequences
Entity
Conceptual Entity
Physical Object
Substance
Anatomical Structure
Manufactured Object
Organism
BioPortal
BioSharing is exploring methods to serve
machine-readable versions of content
metadata standards, via providing
provenance for their elements. The
CEDAR team is working with BioSharing to
inform the creation of metadata templates,
rendering standards invisible to the
researchers.