Tag Archive for: metadata standards

New: YAML Support for CEDAR Artifacts

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We’re excited to announce support for a new YAML-based representation of CEDAR metadata artifacts. YAML (YAML Ain’t Markup Language) offers a more readable, compact alternative to JSON for defining CEDAR templates, elements, fields, and instances—making it easier for users and developers to understand and edit metadata structures.

Why YAML?

CEDAR templates have traditionally been represented as JSON Schema. While powerful and expressive, JSON Schema can be verbose and difficult to read or edit manually—especially for users reviewing or writing complex metadata templates.

The new YAML format addresses this by offering:

  • Improved readability with cleaner indentation and less syntactic clutter
  • Simpler hand-editing of templates for users comfortable with structured configuration formats
  • Better version control diffs (changes in YAML are easier to interpret in Git-based workflows)
  • Easier onboarding for those new to CEDAR or metadata specification

What’s Included

The YAML representation captures the full semantics of CEDAR artifacts, including:

  • Template structure
  • Field definitions and types
  • Value constraints and cardinality
  • Ontology bindings and value sets
  • Required fields and conditional visibility
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New Paper in Scientific Data: How CEDAR Enables Standardized Metadata Across HuBMAP—and Now SenNet

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We’re pleased to announce the publication of a new paper in Scientific Data titled
“Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets”
(Read the paper).

This paper outlines how the CEDAR Workbench has played a central role in ensuring that experiment-related metadata collected by the HuBMAP consortium adheres to FAIR principles and community standards—despite being entered by researchers using spreadsheets. It also describes the expansion of this approach into the SenNet program, demonstrating how metadata consistency and quality can scale across large, decentralized biomedical research consortia.

The Challenge: Researcher-Friendly Interfaces with Standards-Driven Metadata

Biomedical consortia like HuBMAP face a major challenge: researchers need to enter metadata that is rich, precise, and standards-compliant—but they overwhelmingly prefer working in spreadsheets. This poses a tension between usability and data quality.

Rather than force researchers to abandon familiar tools, the CEDAR team collaborated with HuBMAP to design a solution that lets researchers continue using spreadsheets while ensuring the underlying metadata adheres to formal standards.

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NIH CDEs Now Fully Supported in CEDAR for Metadata Authoring

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CEDAR now provides comprehensive support for NIH Common Data Elements (CDEs), making it easier than ever for researchers to incorporate standardized, reusable data definitions into their metadata. With this update, over 28,000 CDEs from the NIH CDE Repository have been ingested, semantically enriched, and published within the CEDAR environment for immediate reuse.

This NIH content complements the existing library of more than 80,000 CDEs from the National Cancer Institute’s caDSR, already accessible in CEDAR through earlier work. Together, these CDEs span a wide range of domains and enable more consistent, interoperable, and FAIR metadata collection across biomedical research projects.

CDEs as First-Class Metadata

CEDAR supports CDEs as structured metadata components, respecting the semantics and specifications defined by ISO/IEC 11179 and NIH practice. In CEDAR’s web-based Template Designer, each CDE includes:

  • Unique identifiers and versioning
  • Structured data types and value domains
  • Enumerated value sets (with ontology mappings via BioPortal)
  • Standardized and alternative question texts
  • Embedded provenance and deployment metadata

Researchers can assemble these CDEs into custom metadata templates without writing code, ensuring semantic consistency and compliance with community standards.

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Empowering Rich Metadata Entry: How Dryad and OSF Are Using the CEDAR Embeddable Editor

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As scientific data sharing becomes increasingly vital to research transparency and reuse, the role of high-quality metadata has never been more important. Yet, creating structured, standards-aligned metadata remains a complex task—especially when researchers are forced to navigate unfamiliar tools or metadata standards outside their everyday workflows. That’s where the CEDAR Embeddable Editor (CEE) steps in.

Developed by the CEDAR team, the CEE is a lightweight, standards-compliant Web Component that enables third-party platforms to embed machine-actionable metadata templates directly into their interfaces. Instead of sending researchers off to external metadata portals, the CEE brings structured metadata authoring directly into the systems where scientists already work—lowering friction, improving consistency, and aligning with the FAIR principles.

Recently, two major research data platforms—Dryad and the Open Science Framework (OSF)—have integrated the CEE to enhance their metadata workflows.

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