An ontology-based Rare Disease Common Data Model harmonising international registry use, FHIR, and the Phenopacket Schema
Attention: The RD CDM paper is currently under review. As soon as it is published, we will update the version to 2.0.0 and provide a link to the paper here. The version 2.0.0.dev0 is the initial release of the RD CDM under review.
The Rare Disease Common Data Model (RD CDM) is designed to harmonize rare disease data capture across international registries. It integrates standards such as the ERDRI-CDS, HL7 FHIR, and GA4GH Phenopacket Schema, creating a scalable, ontology-driven framework that supports advanced interoperability for research and care. The RD CDM Version 2.0.0 consists of 78 data elements, extending the ERDRI-CDS and allowing deeper insights into genetic findings, phenotypic features, and family history of individuals.
- Interoperability: Aligns with HL7 FHIR v4.0.1 and GA4GH Phenopacket v2.0 for structured data exchange.
- Ontology-driven: Utilizes ontologies such as SNOMED CT, LOINC, MONDO, OMIM, and HPO for standardizing rare disease terminologies.
- Modular Structure: Comprises essential data elements categorized into formal criteria, personal information, patient status, disease, genetic findings, phenotypic findings, and family history.
- Cross-registry Compatibility: Enables data reuse across multiple registries with consistent encoding and semantic alignment.
This section provides instructions for getting started with the RD CDM. For more detail please read our Documentation
- Python 3.x
- Dependencies in requirements.txt
- Clone the repository
git clone https://github.com/BIH-CEI/rd-cdm.git
cd rd-cdm- Install dependencies:
pip install -r requirements.txt- Run tests to validate the JSON schema:
pytest tests/Contributions are welcome! Please feel free to create issues, discuss features, or submit pull requests to help enhance this project. For larger contributions, consider reaching out to discuss collaboration opportunities.
- Human Phenotype Ontology 🔗
- Monarch Initiative Disease Ontology 🔗
- Online Mendelian Inheritance in Man 🔗
- Orphanet Rare Disease Ontology 🔗
- SNOMED CT 🔗
- ICD 11 🔗
- ICD10CM 🔗
- National Center for Biotechnology Information Taxonomy 🔗
- Logical Observation Identifiers Names and Codes 🔗
- HUGO Gene Nomenclature Committee 🔗
- Gene Ontology🔗
- NCI Thesaurus OBO Edition 🔗
For the versions used in a specific RD-CDM version, please see the resources in our documentation.
This project is licensed under the terms of the MIT License
We would like to extend our thanks to all the authors involved in the development of this RD CDM model.
- Authors:
- Adam SL Graefe
- Filip Rehburg
- Miriam Hübner
- Steffen Sander
- Prof. Peter N. Robinson
- Prof. Sylvia Thun
- Prof. Oya Beyan