LinkML in Rare Diseases: Ontology-Based Interoperability for Clinical Registries and Analysis

Adam Graefe

LinkML community call

Thursday, 16^th of January 2026

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LinkML community call – 15^th of January 2026 | Adam Graefe

Interoperability

• Semantic Interoperability

Shared and precise interpretation of medical data

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• Syntactic Interoperability

Communication via compatible formats and protocols

LinkML community call – 15^th of January 2026 | Adam Graefe

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MII

IPS

FHIR

Genomics Reporting

EHDS

Patient

Observation

Condition

Specimen

Location

Practitioner

Procedure

Device

Encounter

Episode of Care

Account

Health Level 7

Fast

Healthcare

Interoperability

Resources

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Hospital Information Systems

int. RD-CDM

LinkML community call – 15^th of January 2026 | Adam Graefe

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FHIR

Genomics Reporting

EHDS

IPS

MII

Abaza H et al .Domain- Specific Common Data Elements for Rare Disease Registration: Conceptual approach of a European Joint Initiative toward Semantic Interoperability in Rare Disease research. JMIR Medical Informatics. 2022 May 20;10(5):e32158. https://doi.org/10.2196/32158

https://eu-rd-platform.jrc.ec.europa.eu/set-of-common-data-elements_en (Accessed 25.07.2025)

int. RD-CDM

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

https://www.nature.com/articles/s41587-022-01357-4

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

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Analysis

int. RD-CDM

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

IPS

Genomics Reporting

MII

EHDS

https://github.com/BIH-CEI/rd-cdm

int. RD-CDM

Common Data Set

LinkML community call – 15^th of January 2026 | Adam Graefe

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data_elements.yaml

rd_cdm_v2_0_2.yaml

value_sets.yaml

code_systems.yaml

rd_cdm.yaml (root class)

>_ rd-cdm-merge

rd_cdm_v2_0_2.json

rd_cdm_v2_0_2.csv

>_ rd-cdm-json

(LinkML loaders)

>_ rd-cdm-csv

rd_cdm_pydantic.py

rd_cdm.py

LinkML runtime

LinkML pydantic gen.

>_ rd-cdm-validate

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

IPS

Genomics Reporting

MII

EHDS

int. RD-CDM

https://www.nature.com/articles/s41597-025-04558-z

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

RareLink-CDM

LinkML schema

REDCap instruments

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Local REDCap site

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FHIR resources

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Hospital Information System

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Registry Linkage

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Analysis

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Phenopackets

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A local rare disease �cohort / registry site

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Prospective RD data

Genomics �Reporting

R4

2.0

Manual Data Capture Guide

Semi-Automated �Import (LinkML Map)

CDIS Module

toFHIR �Module

RareLink- �Phenopackets Module

Retrospective (tabular) data

RD-CDM

LinkML community call – 15^th of January 2026 | Adam Graefe

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RareLink- Phenopackets engine

IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

RareLink-CDM

LinkML schema

REDCap instruments

REDCap data �dictionary

LinkML schema definitions

REDCap instruments�(variables & choices�w/ embedded ontologies)

Meta schema

Code systems

Repeated elements

Custom data �models�& disease-�specific �extensions

LinkML�validate

Corresponding �Pydantic &

Python classes

RD-CDM

Raw REDCap �cohort data

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Phenopackets

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LinkML community call – 15^th of January 2026 | Adam Graefe

IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

https://rarelink.readthedocs.io/

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

Undiagnosed �Disease �Programme

LinkML community call – 15^th of January 2026 | Adam Graefe

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IPS

EHDS

IPS

Genomics Reporting

MII

int. RD-CDM

https://www.nature.com/articles/s41525-025-00534-z

LinkML community call – 15^th of January 2026 | Adam Graefe

Ideas and next steps

• Improved automation for RD-CDM and RareLink
• LinkML-based rare disease templates for new/existing data models and cohorts
• Ongoing and new collaborations with clinical RD registries globally
• Exchange and alignment with international entities (HL7, GA4GH, GDI, JARDIN, etc.)
• Better integration and use of further LinkML tools and OAK
• Deep integration of agentic LLM tools (i.e. ai4curation, etc.) for REDCap�

🡪 Open-source and community-based: �we’re happy to collaborate and look forward to feedback!

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LinkML community call – 15^th of January 2026 | Adam Graefe

Thank you very much!����

adam.graefe@charite.de

LinkML community call – 15^th of January 2026 | Adam Graefe