RareLink

Rare Disease Interoperability Framework in REDCap linking Registry Use, HL7 FHIR® and the GA4GH Phenopacket Schema©

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Table of Contents

• Project Description
• Features
• Getting Started
  • Prerequisites
  • Installation
• Contributing
• Resources
• License
• Acknowledgements

Project Description

RareLink - A Rare Disease Interoperability Framework in REDCap to enable Registry Use, HL7 FHIR® and the GA4GH Phenopacket Schema© including comprehensive documentation for data management and user guides. This includes data capture, import, export, project set up and and is ready for clinical use management in clinical care or research.

Features

REDCap is a widely-used clinical electronic data capture system, licensed by numerous university hospitals and institutions worldwide. RareLink provides detailed specifications on how REDCap sheets and data should be structured and encoded to ensure seamless integration with both the HL7 FHIR and GA4GH Phenopacket pipelines. RareLink is built upon the Rare Disease Common Data Model v2.0, with all functionalities preconfigured for ease of use. For disease-specific extensions, such as Domain Specific Data Elements, we offer clear rules and specifications to facilitate the development of additional REDCap sheets, ensuring their seamless integration into RareLink's preconfigured data pipelines.

RareLink integrates the following features for Rare Disease data management in REDCap:

1. Native REDCap usage: downloadable REDCap forms of all RD CDM sections including documentation and manuals for installing and setting up your local REDCap project, manual data capture guides, connecting BioPortal.
2. Semi-Automated Data Capture (from Tabluar Data) with OntoBridge: Our RD CDM is defined as an SQL-based common data model for OntoBridge usage. This allows the syntactic mapping of existing tabular data bases with our RD CDM. While the semantinc mapping and encoding must be done locally, we provide guidelines on how to process your local data according to our specifications. This enables the subsequent validation, upload to your local REDCap project, and the usage of the HL7 FHIR and GA4GH Phenopacket pipelines.
3. GA4GH Phenopacket Mapper: RareLink utilises the Phenopacket Mapper and predefines its configuration for all native RareLink REDCap instruments that allow the procesing of the entire RD CDM viable for Phenopacket export. To allow for data capture around the RD CDM, we provide precise guidelines on how to develop REDCap instruments and sheets, specifically the encoding of all variables and data elements, to also enable the data export to validated Phenopackets.
4. Automated Export to local HL7 FHIR Resources or HL7 FHIR server: utilising the integrated toFHIR Module, RareLink provides the preconfiguration for all native RareLink REDCap instruments that allow the procesing of the entire RD CDM viable for HL7 FHIR v4.0.1 export.

Getting Started

Instructions on how to set up and run your project locally please read the docs here(tbc). To provide a short overview:

1. Set up your local REDCap license and project, if desired using RareLink's project set up
2. Install packages necessary and activate REDCAp API for you project
3. Run the installation packages defined for the specific functionalities you want to use linked to your local REDCap API.
4. Run the functionalities you need to generate HL7 FHIR resources or GA4GH Phenopackets.

Prerequisites

You need a local REDCap license and REDCap server running. For more information please see: https://projectredcap.org/partners/join/

Installation

RareLink REDCap Project

RareLink provides an entire REDCap project structure that can be downloaded here. For more information please see our documenation here.

Semi-Automated Import from existing tabular data bases

To process and capture existing local tabular data bases of rare disease data using OntoBridge please see our detailed user guide here

Generation of HL7 FHIR v4.0.1 Resources

To generate HL7 FHIR Resources, please find more information in our documentation here

Phenopackets Pipeline

To utilise the RareLink configuration of the Phenopacket Pipeline for the native RareLink sheets, or other REDCap data, please find detailed information here.

Contributing

Please write an issue or exchange with other users in the discussions if you encounter any problems or wish to give feedback. Feel free to reach out to us, if you are interested in collaborating and improve the use of REDCap for rare disease research and care.

Resources

Ontologies

• Human Phenotype Ontology (HP, Version 2024-08-13) 🔗
• Monarch Initiative Disease Ontology (MONDO, Version Version 2024-09-03) 🔗
• Online Mendelian Inheritance in Man (OMIM, Version 2024-09-12) 🔗
• Orphanet Rare Disease Ontology (OPRHA, Version 2024-09-12) 🔗
• National Center for Biotechnology Information Taxonomy (NCBITaxon, Version 2024-07-03) 🔗
• Logical Observation Identifiers Names and Codes (LOINC, Version 2.78) 🔗
• HUGO Gene Nomenclature Committee (HGNC, Version 2024-08-23) 🔗
• Gene Ontology (GENO, Version 2023-10-08) 🔗
• NCI Thesaurus OBO Edition (NCIT, Version Version 24.04e ) 🔗

Submodules

• toFHIR
• Phenopacket Mapper
• OntoBridge

License

This project is licensed under the terms of the MIT License

Acknowledgements

We would like to extend our thanks to ... for his support in the development of this project.

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• Authors:
  • Adam Graefe
  • Filip Rehburg
  • Daniel Danis, PhD
  • Prof. Peter N. Robinson
  • Prof. Sylvia Thun
  • Prof. Oya Beyan