Schema Documentation

This section describes the LinkML schemas used in the CDE Harmonization project.

Overview

The project converts CDEs from various repositories into LinkML schemas, creating what we call “Condor microschemas”. These schemas provide:

• Structured representation of CDEs

• Type definitions and constraints

• Ontology bindings and mappings

• Permissible values (enumerations)

Available Schemas

• NIH NLM CDE Schema
  • Overview
  • Schema Details
  • Structure
  • Usage
  • Files
• PhenX CDE Schema
  • Overview
  • Schema Details
  • Structure
  • Usage
  • Files
• RADx-UP CDE Schema
  • Overview
  • Schema Details
  • Structure
  • Data Dictionary
  • Usage
  • Files

Schema Components

Each CDE schema typically includes:

Classes

Represent data collection forms or surveys

Slots

Individual data elements (questions, measurements)

Enumerations

Permissible values for categorical fields

Types

Data types with constraints

Prefixes

Ontology and vocabulary namespaces

Working with Schemas

Schemas are stored in the linkml/ directory as YAML files:

• nih_nlm_schema.yaml - NIH NLM CDEs

• phenx_schema.yaml - PhenX CDEs

• radx_up_schema.yaml - RADx-UP CDEs

See the How-To Guide section for guides on using these schemas.