CDE Harmonization Documentation

Welcome to the CDE Harmonization project documentation. This project supports the harmonization of Common Data Elements (CDEs) to enable interoperability across clinical research studies.

Overview

CDEs are standardized data fields and survey questions with defined permissible values that facilitate consistent data collection. Despite their widespread use, CDEs remain fragmented across multiple repositories, lack semantic bindings to ontologies, and are often incompatible with one another—limiting cross-study integration and AI-readiness.

Our goal is to transform CDEs and study-specific variables into computable, semantically rich, and interoperable data assets using the LinkML framework, AI-assisted curation, and ontology-based standardization.

Documentation

Contents:

• Overview
  • What is CDE Harmonization?
  • The Problem
  • Our Approach
  • Repository Contents
  • Impact
• Installation
  • Prerequisites
  • Installing from Source
  • Verifying Installation
  • Dependencies
  • Data Access
  • Development Installation
  • Next Steps
• Schema Documentation
  • Overview
  • Available Schemas
  • Schema Components
  • Working with Schemas
• How-To Guide
  • Collecting and Converting CDEs
  • Converting CDEs to LinkML
  • Future Workflows
• Project Roadmap
  • Current Status
  • Planned Development
  • Timeline
  • Technology Stack
  • Get Involved
  • References

Key Technologies

• LinkML: Schema language for defining computable, semantically rich data models

• SSSOM: Standard for representing and sharing ontology and CDE mappings with provenance

• Ontologies: HPO (phenotypes), Mondo (diseases), LOINC (lab tests), OBA (biological attributes)

• AI/LLM tools: CurateGPT, AI4Curation, and semantic embeddings for automated mapping and curation

Project Links

• GitHub Repository

• LinkML Framework

• SSSOM Mappings

Indices and tables

• Index

• Module Index

• Search Page