RareLink Overview

Tip

Manuscript: RareLink was recently published in npj Genomic Medicine: https://www.nature.com/articles/s41525-025-00534-z

RareLink aims to maximise the utility of REDCap by providing a comprehensive framework designed specifically for rare disease (RD) research and care. At the core of RareLink is this documentation, the RareLink instruments that are based on the RD-CDM, its user guides and the surrounding preconfigured pipelines and software architecture. This framework ensures that data capture is both consistent and compliant with HL7 FHIR and GA4GH Phenopackets, without the need for additional coding or mapping. As a result, RareLink allows researchers and clinicians to collect and process RD data seamlessly within the REDCap environment.

../_images/rarelink_overview.png — Overview of the RareLink framework integrated with a local REDCap instance. The framework comprises the REDCap instruments based on the RD-CDM, the RareLink API, the toFHIR & CDIS module for export and import to HL7 FHIR IPS and Genomic Reporting Resources, and the RareLink-Phenopackets module for direct export to GA4GH Phenopackets. Additionally, the LinkML-based import mapper facilitates data import from tabular databases into REDCap, while the Manual Data Capture Guide assists with the manual data capture of RD-CDM data in a local REDCap project. The framework is also configurable for disease-specific extensions or custom data models.

Note

You will need your own REDCap instance to deploy the RareLink framework. See the Set up a REDCap Project for more information.

RareLink Framework components

../_images/rarelink_core_modules.png — Overview of the five RareLink core RareLink modules.

Semi-Automatic Import

In many Rare Disease specialised centres, registries or hospitals, data is stored in tabular databases (e.g. Excel). RareLink’s Import Mapper that is utilising the Phenopacket Mapper API can be used to convert and import data from these databases into the REDCap RareLink format and your local REDCap project.

Continue here…

Guide for the Set up the REDCap API.

User guide for Semi-Automatic Import.

Manual Data Capture

RareLink provides a preconfigured data collection sheets based on the RD-CDM and user guides for manual data capture to ensure precision and correctness of data captured. Further, RareLink defines guidelines for developing more specialised REDCap sheets around the RD-CDM so that the data captured can also be processed by our framework to generate FHIR Resources and Phenopackets.

Continue here…

Guide to install the Set up the RareLink Framework.

Guide to develop the Set up a REDCap Project.

User guide for Manual Data Capture.

Local REDCap Project Setup and API

RareLink is designed to be deployed and installed in a local REDCap instance. Using the guidelines provided, or using our preconfigured RareLink-REDCap and setting up the RareLink API, you can ensure that the data captured is compliant with the our framework to generate FHIR Resources and Phenopackets.

Continue here…

How to Set up the Data Dictionary.

How to deploy and Set up the REDCap API.

RareLink & Phenopackets

RareLink utilises the Phenopacket Mapper to convert the data captured in REDCap into Phenopackets. The RD-CDM and the corresponding RareLink instruments are preconfigured within our GitHub repository to generate Phenopackets automatically.

Continue here…

How to set up the Set up the RareLink Framework and the Set up the REDCap API.

Guide to Phenopackets Module.

Phenopacket Mapper Repository: https://github.com/BIH-CEI/phenopacket_mapper

Documentation: https://bih-cei.github.io/phenopacket_mapper/latest/

RareLink & toFHIR

RareLink utilises toFHIR from SRDC to convert the data captured in REDCap into FHIR Resources. The RD-CDM and the corresponding RareLink instruments are preconfigured within our GitHub repository to generate International Patient Summary (IPS) v2.0, Genomoic Reporting v3.0.0, and FHIR v4.0.1-base profile compliant FHIR Resources automatically. Below you can find more information on how to set up the RareLink API and toFHIR module in your local REDCap project to generate FHIR Resources.

Continue here…

How to set up the Set up the RareLink Framework and the Set up the REDCap API.

Guide to FHIR Module.

toFHIR Repository: https://github.com/srdc/tofhirs

Website: https://onfhir.io/tofhir/

RareLink & FHIR Import

RareLink provides a detailed guide on how to link a FHIR server and import FHIR Resources into REDCap utilising the REDCap modules Clinical Data Interoperability Services (CDIS). This module must be installed and activated at your local REDCap site by the REDCap administrator. The guide includes a step by step guide on how to import FHIR Resources into REDCap and how to map the FHIR Resources to the RD-CDM.

Continue here..

CDIS REDCap: https://projectredcap.org/software/cdis/

CDIS Paper: https://doi.org/10.1016/j.jbi.2021.103871

User guide for Importing FHIR to REDCap