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Background

  • Rare Diseases and Interoperability
    • Definitons
    • Further Reading
  • Ontologies & Terminologies
    • Ontologies used in RareLink
    • Further Reading
  • GA4GH Phenopackets
    • Phenopacket Blocks
    • Phenopacket Tools
  • HL7 FHIR
    • FHIR and Rare Diseases (RDs)
    • FHIR Overview - Clinicians
    • FHIR Overview - Developers
    • FHIR Overview - Architects
    • Further Reading
  • RD-CDM
    • RD-CDM Overview
    • Key Success Factors of a Rare Disease Common Data Model
    • Further Reading
  • REDCap
    • REDCap Projects
    • REDCap Instruments
    • REDCap Data Dictionary
    • REDCap API
    • REDCap Ontology Services
    • Further Reading

RareLink Framework

  • RareLink Overview
    • RareLink Framework components
  • RareLink-CDM
    • Contents
    • REDCap Data Dictionary
    • LinkML Schema
    • Rules for REDCap codes and codesystems
    • REDCap Field Annotations
    • RareLink-CDM Instruments
  • RareLink CLI
    • 1. Framework Setup (framework)
    • 2. REDCap Setup (setup)
    • 3. REDCap Tools (redcap)
    • 4. FHIR configuration and pipelines (fhir)
    • 5. Phenopacket Export (phenopackets)

Installation

  • Set up the RareLink Framework
    • Getting Started
    • RareLink Framework CLI config
  • Set up a REDCap Project
    • Steps
    • Next Steps and further reading
    • RareLink CLI Commands
  • Set up the Data Dictionary
    • Installation
    • Separate RareLink-CDM Instruments
    • Extensional RareLink-CDM Instruments
    • Customise the Data Dictionary
  • Set up the REDCap API
    • API Set Up

User Guide

  • Manual Data Capture
    • General Information (please read!)
    • (1) Formal Criteria
    • (2) Personal Information
    • (3) Patient Status
    • (4) Care Pathway
    • (5) Disease
    • (6.1) Genetic Findings
    • (6.2) Phenotypic Features
    • (6.3) Measurements
    • (6.4) Family History
    • (7) Consent
    • (8) Disability
  • Semi-Automatic Import
    • Overview of Components
    • Steps When Importing Data
    • Examples
    • Additional Resources
  • Phenopackets Module
    • Get started
    • RareLink-CDM to Phenopackets
    • RareLink-Phenopacket engine
    • All Command-Line Options
    • Mapping Configuration Structure
    • Advanced Configuration Options
    • Mapping Strategies
    • Best Practices
  • Phenopacket Adapters
    • Multi-Onset Adapter
    • Ontology Routing Adapter
  • FHIR Module
    • Getting started
    • RareLink-CDM FHIR Profiles
    • RareLink-CLI FHIR Commands
    • Docker Commands
    • Importing FHIR to REDCap
  • Develop REDCap Instruments
    • REDCap instrument structure
    • REDCap-inherent rules
    • RareLink obligatory rules
    • RareLink optional rules
  • REDCap Tools
    • API Endpoints

Additional Information

  • Contributing
  • Changelog
    • v2.0.6
    • v2.0.5 (2025-12-12)
    • v2.0.4 (2025-09-25)
    • v2.0.3 (2025-09-24)
    • v2.0.2 (including v2.0.1)
    • v2.0.0
    • v2.0.0.dev1 (Under Development)
    • Previous versions (up to v2.0):
  • FAQ
  • Glossary
  • Acknowlegements
  • License
  • Contact
RareLink REDCap Documentation
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