CEDAR: Easing Authoring of Metadata to Make Biomedical Data Sets More Findable and Reusable

Presenting Author Information 

Name

Debra Willrett

Institution

Stanford Medicine, Center for Biomedical Informatics Research

BD2K Grant Number

U54 AI117925

PI

Mark A. Musen

Email

willrett@stanford.edu

Phone Number

4087724310

Additional Author Information 

Names and affiliations of additional authors

(one per line)

John Campbell, Northrop Grumman, Inc. 
Kei-Hoi Cheung, Yale University 
Michel Dumontier, Stanford University
Kim A. Durante, Stanford University
Attila L. Egyedi, Stanford University
Olivier Gevaert, Stanford University
Rafael Gonçalves, Stanford University
Alejandra Gonzales-Bertran, Oxford University
John Graybeal, Stanford University
Purvesh Khatri, Stanford University
Steven H. Kleinstein, Yale University 
Csongor I. Nyulas, Stanford University
Maryam Panahiazar, Stanford University
Philippe Rocca-Serra, Oxford University
Marcos Martínez-Romero, Stanford University
Susanna-Assunta Sansone, Oxford University
Ravi D. Shankar, Stanford University
Mark A. Musen, M.D., Ph.D. Stanford University

Is there an additional contact person?

Yes

Name of additional contact

Martin O' Connor

Email address of additional contact

martin.oconnor@stanford.edu

Additional information 

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Abstract Title

CEDAR: Easing Authoring of Metadata to Make Biomedical Data Sets More Findable and Reusable

Abstract Description

Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working with these standards are significant. The Center for Expanded Data Annotation and Retrieval (CEDAR) is building an end-to-end system to ease the authoring of metadata and the templates. This system targets the creation of higher quality metadata to facilitate data discovery, interoperability, and reuse. With our public release in September 2016, we now support many new features which make authoring easier.

Template and Metadata Repository: We developed a standardized representation of metadata and the templates that describe them, together with Web-based services to store, search, and share these resources. Templates created using CEDAR technology are stored in our openly accessible community repository, and can now be shared with other people and groups. Researchers can search for templates to annotate their studies, and share their metadata with others. We’ve now added Web-based interfaces and REST APIs to facilitate access to templates, and all the metadata collected using those templates.

Template and Metadata Editor: We developed highly interactive Web-based tools to simplify the process of authoring metadata and templates. The Template Editor allows users to create, search, and author templates. An upgraded feature provides interoperation with ontologies: interactive look-up services linked to NCBO’s BioPortal (bioportal.bioontology.org) let template authors find ontology terms to annotate fields in their templates and to define possible values of fields, including creating new terms and value sets. The Metadata Editor, which creates a forms-based acquisition interface from a template, has been redesigned so users can more easily populate metadata based on the template fields.