What’s going on related to CEDAR?

Diagram of the CEDAR template model: community standards are formalized as template fields, elements, and templates, populated as metadata instances that describe datasets.

New Paper in AI Magazine: Knowledge Engineering for Open Science

/in /by

We’re pleased to announce the publication of a new paper in AI Magazine titled “Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards.”

Synthesizing ten years of CEDAR research, the paper makes the case that the metadata templates at the heart of CEDAR are a modern form of declarative knowledge base—capturing, in symbolic form, how a community of scientists believes its data should be described so that datasets can be findable, accessible, interoperable, and reusable (FAIR).

The Big Idea: Metadata Standards as Knowledge Bases

Decades ago, hand-built knowledge bases powered intelligent systems by encoding expert knowledge in an inspectable, editable form. The paper argues that CEDAR templates play the same role for open science: they encode a community’s metadata reporting guidelines as machine-actionable templates that enumerate the attributes of an experiment and link those attributes to ontologies and value sets. Unlike patterns learned from data, these standards often don’t yet exist in any “learnable” form—so capturing them still requires the careful, expert-driven knowledge engineering the field has practiced for decades.

Read more

CEDAR 2.8.0 Now Live: RRID and PubMed ID Field Support

/in , /by

This latest update strengthens CEDAR’s ability to support rich, standardized scientific metadata through the addition of new external authority field types.

What’s New

RRID Field Support
CEDAR now supports the RRID (Research Resource Identifier) field type. Template authors can include RRID fields in their templates and instances, allowing users to record standardized identifiers for reagents, tools, and model organisms. This enhancement improves metadata consistency, reproducibility, and interoperability across datasets.

PubMed ID Field Support
CEDAR now provides a PubMed ID field type for linking scientific publications directly within metadata instances. Authors can reference PubMed IDs to automatically connect to the corresponding publications in PubMed, streamlining citation management and ensuring clear traceability to supporting literature.

Learn More

For more information about CEDAR features, visit the CEDAR manual or explore our GitHub repository.

CEDAR 2.7.11 Now Live: PFAS Field Support and Embedded Editor Improvements

/in , /by

We’re pleased to announce that CEDAR 2.7.11 has been successfully deployed to production. This release brings important improvements to the metadata authoring experience and introduces support for additional field types.

What’s New

PFAS Field Availability
CEDAR now supports the new PFAS (Per- and Polyfluoroalkyl Substances) field. Template authors can incorporate PFAS-related metadata fields directly into their templates and instances, enabling richer environmental and chemical data modeling within CEDAR.

Embedded Editor as the Default
The CEDAR embedded instance editor is now the default editing experience in the Workbench. This editor offers a more integrated, streamlined approach to instance editing, improving responsiveness and simplifying the user interface.

Read more

New: YAML Support for CEDAR Artifacts

/in /by

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
Read more