bih-cei/raredif

Rare Disease Interoperability Framework enabling HL7 FHIR, GA4GH Phenopackets, and registry linkage

RareDIF

Rare Disease Interoperability Framework in REDCap enabling HL7 FHIR® and the GA4GH Phenopacket Schema©

Stable Documentation
Latest Documentation

Table of Contents

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

Project Description

RareDIF (Rare Disease Interoperability Framework) is a comprehensive framework in REDCap for rare disease data management in clinical care or research. It enables data capture, processing, import and export to the international interoperability standards HL7 FHIR® and the GA4GH Phenopacket Schema©.

Features

REDCap is a clinical electronic data capture system, for which many university hospitals have licenses. RareDIF bases on our Common Data Model for Rare Diseases based on the ERDRI-CDS, HL7 FHIR, and GA4GH Phenopackets. Our data model can be found in our ART-DECOR project RD CDM (you may need to deactivate your adblock for this website). For disease-specific data capture and analyses, recommendations to extend our RD CDM are given here (tbc). For further information regarding DCDEs (Domain Specific Data Elements) please read: https://pubmed.ncbi.nlm.nih.gov/35594066/

This framework encompasses the following features for RD data management:

1. Native REDCap usage: downloadable REDCap forms of all RD CDM sections, documentation and manuals for installing and setting up your local REDCap project, manual data capture guides, connecting BioPortal, and preparing your REDCap API
2. Semi-Automated Data Capture (from Tabluar Data): Utilities and manuals mapping tabular data to the RD CDM, including a user-friendly GUI, API connection, and clear instructions for each section
3. GA4GH Phenopacket Pipeline: generating validated GA4GH Phenopackets of all RD CDM possible, connected with an API, a GUI and precise documentation. So far, this work is based on the ERKER2Phenopackets Pipeline.
4. Automated Export to local HL7 FHIR Resources or HL7 FHIR server: utilising the integrated toFHIR Module, generating local HL7 FHIR Resources generated from REDCap forms with automated export and record linkage with existing HL7 FHIR servers.
5. Automated import of HL7 FHIR resources to RECap: HL7 FHIR resources are automatically imported to a local REDCap project & database using the CDIS-Module.

For further use of GA4GH Phenopackets© please read: https://www.nature.com/articles/s41587-022-01357-4.

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
2. Install packages necessary and activate REDCAp API for you project
3. Run the installation packages defined below 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

Software, libraries, or dependencies that need to be installed before setting up the project can be found in detail in our docs here. As a brief overview you need the following:

Installation

tbc.

RareDIF REDCap Project

tbc.

(Semi-)Automated Import Scripts

tbc.

HL7 FHIR Modules

tbc.

Phenopackets Pipeline

tbc. For the time being, please see more details in our previous GitHub Repository ERKER2Phenopackets

Contributing

Please write an issue or exchange with other users in the discussions if you encounter any problems. 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: 2023-06-06) 🔗
• Online Mendelian Inheritance in Man (OMIM, version: 2023-09-08) 🔗
• Orphanet Rare Disease Ontology (OPRHA, version: 2023-09-10) 🔗
• National Center for Biotechnology Information Taxonomy (NCBITaxon, version: 2023-02-21) 🔗
• Logical Observation Identifiers Names and Codes (LOINC, version: 2023-08-15) 🔗
• HUGO Gene Nomenclature Committee (HGNC, version: 2023-09-10) 🔗
• Gene Ontology (GENO, version: 2023-07-27) 🔗

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

raredif's Issues

Boilerplate for Mapping Utils

A1) Develop repeatable forms for the 1...n sections

Create milestones and issues for Epic A

Epic A1) Development of forms for all sections of RD CDM

• #18
• define all elements in field annotations
• include comments and instructions if necessary
• consider ActionTags and BranchingLogic

Example GUI for Mapper

create test data for Epic B

create semi realistic excel sheet with fake data
upload to res file

put all RD CDM tables into res

pdf oder word

project management

markdown into "res" file from obsidian.md file

A2) Prepare REDCap API

• Activate API for local REDCap project
• read requirements for API usage and implementation
• create development overview for implementation in Epic B - E

define milestones for D) & E)

talk with Samer
define them

Fetch dataset from REDCap option

Instead of taking a file also allow for the user to immediately fetch their dataset through the REDCap API

A3) REDCap User Docs

• Docs: general implementation and usage of framework
• installation of REDCap forms (repeatable, connecting BioPortal, etc.)
• prepare template structure in Docs for Epic B - E
• SOP: Manual Data Capture of entire form (including e.g. HGVS validation)

Test Cases for Mapping Utils