CEDAR Technologies for AIRR Submissions

1. BioSample
BioProject
SRA
AIRR
Community
The CEDAR Workbench offers web services
enabling easy metadata model creation and
submission of biomedical metadata.
Use REST APIs to create, share, and
submit quality metadata resources
AIRR community members from
Yale University worked as part
of the CEDAR team to create
matching CEDAR templates.
The CEDAR AIRR template
combines metadata for 3 NCBI
repositories in one template.
CEDAR provides a versatile
tool that associates metadata
with ontology terms from the
BioPortal ontology repository.
Once AIRR
templates are
approved, CEDAR
templates will be finalized.
Resulting metadata are also
available as JSON, JSON-
LD, or RDF for easy reuse.
Use the CEDAR Workbench for
free! Review the source code in
GitHub (metadatacenter project).
CEDAR Technologies for AIRR Submissions
Syed Ahmad Chan Bukhari*1, John Graybeal*2, Martin J. O'Connor2, Marcos Martínez-Romero2, Attila L. Egyedi2, Debra Willrett2, Steven H. Kleinstein1, Kei-Hoi Cheung3, Mark A. Musen2
…
cedar.metadatacenter.org
Members of the AIRR
community developed an
AIRR metadata
specification and a set of
templates for NCBI’s
BioProject, BioSample,
and SRA repositories.
Metadata
Repository
Metadata
Repository
Template authors precisely
define template fields,
controlling how users see
them and fill them out.
Submit related data files
through CEDAR to the
NCBI SRA repository
—with your metadata!
Babraham Bioinformatics
Stefani Billings @ Stanford Magazine
CAIRR
resource.metadatacenter.org/api github.com/metadatacenter
CAIRR Workflow
Metadata entries can be
updated over time until
ready for submission.
Folders,
Groups &
Permissions
(Neo4j DB)
Users
(MongoDB)
= Third-party components
= CEDAR components
Storage
user profiles user authorization
User
Service
Template
Service
Value
Recommender
Service
Auth. Service
(Keycloak)
Open Services
user management resource management intelligent
authoring
controlled terms
Resource
Service
Workspace
Service
= Only internal access
Group
Service
Worker
Service
Queues &
Caching
(Redis)
Submission
Service
Metadata CreatorTemplate Designer Resource Manager
metadata
export
db1
db2
dbn
…
Public Databases
NCBO BioPortal
Open Services
Terminology
Service
Messaging
Service
Messages
(MySQL)
Search Engine
(Elasticsearch)
messages
Metadata Editor
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
Resource Manager
https://cedar.metadatacenter.org/dashboard?folderId=https:%2F%2Frepo.metadatacenter.org%2Ffolders%2F232ab017-ec1e-4…
Template Designer
https://cedar.metadatacenter.org/templates/edit/https://repo.metadatacenter.org/templates/ab105771-564e-42a1-9be4-5a63891…
Metadata
Repository
(MongoDB)
Templates Elements Fields Metadata
Template Model
Submissions go to NCBI—
and status messages are
returned to CEDAR!
Auto-completion and intelligent
suggestions improve speed and
accuracy of metadata entries.
And track our progress in Waffle!
waffle.io/metadatacenter/cedar-projectmetadatacenter.org
CEDAR is supported by the
National Institutes of Health
through the NIH
Big Data to Knowledge program grant.
(Grant Number 1U54AI117925)
CEDAR will conduct
formal trials of the
CAIRR pipeline
in early 2018.
Sign up!
* co-first authors 1. Department of Pathology, Yale School of Medicine, New Haven, CT, USA 2. Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA 3. Department of Emergency Medicine and Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA3
Decem
ber2017
https://m
etadatacenter.org/cairr-poster