CEDAR Technologies for AIRR Submissions

The CEDAR team produced the enclosed poster to support the AIRR Community Meeting III December 3-6, 2017 in Rockville, MD. The poster illustrates the intersection of AIRR community standards (top) with the CEDAR Workbench (bottom), resulting in a custom CEDAR-supported workflow (CAIRR) across the middle of the diagram.

Abstract: The Center for Expanded Data Annotation and Retrieval (CEDAR) has released the CEDAR Workbench, a set of web services enabling easy model creation and submission of biomedical metadata. The software provides user interfaces and REST APIs to create, share, and manage high-quality metadata resources, and to submit those resources to selected repositories. CEDAR is partnering with members of the AIRR community from Yale University to develop an AIRR-specific set of templates and submission capabilities, and will be conducting formal evaluations of this submission pipeline in early 2018. The system's semantic and metadata capabilities include several features that will be particularly applicable to AIRR submissions, as well as many general user capabilities that are optimized for any domain.

The CEDAR Workbench provides a versatile environment for authoring metadata that are coupled with terms from ontologies, obtained from Stanford's BioPortal ontology repository. Template authors can precisely define the fields in the template, controlling how they appear and how they can be filled out by metadata providers. Metadata entries can be updated over time until they are ready for submission. Once the AIRR templates and features are validated and approved, the metadata can be submitted with the corresponding data to the NCBI SRA repository. The resulting metadata are also available via the API as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. In addition to filling out and managing forms via the user interface, users can also leverage our APIs directly to validate metadata, share them, and submit them to external repositories.

The CEDAR Workbench is freely available to use, and the software is available as open source on GitHub in the metadatacenter project. Other information on CEDAR can be found at its web site, https://metadatacenter.org.

Release Date: 
January 29, 2018
CEDAR AIRR Community Meeting III Poster
Author List: 
Syed Ahmad Chan Bukhari*, John Graybeal*, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, Steven H. Kleinstein, Kei-Hoi Cheung, Mark A. Musen
Artifact Type: 
Last Updated: 
Jan 29 2018 - 3:47pm