Open source · FAIR · Federated · GDPR-compliant

Make your research data FAIR from day one

SHaReD is a modular, containerized and federated platform for deterministic FAIRification and integration of heterogeneous biomedical research data.

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164+
Database tables
95%
Storage footprint reduction*
6
Omics modalities
as of 22 Jul 2026
5
Pipelines supported
as of 22 Jul 2026
* Compared to storing raw FASTQ files.
Design principles

Three principles, one coherent ecosystem

SHaReD is built around three orthogonal design principles that together make FAIR compliance a native property of your research data — not an afterthought.

01 — Deterministic FAIRification
Semantic annotation at acquisition
Ontology-constrained annotation at the point of data generation. No post-hoc inference, no probabilistic mapping. Explicit provenance from day one.
02 — Subject-centric model
Every observation anchored to a subject
Clinical, molecular and functional data unified around the biological subject — patient, experimental organism or cellular system — not around files or projects.
03 — Federated infrastructure
Interoperability without centralization
Raw data stays under institutional governance. Semantic knowledge becomes interoperable across distributed environments without moving multi-terabyte files.
Features

Everything you need, nothing you don't

From ontology-guided data entry to nf-core pipeline import, SHaReD covers the full research data lifecycle.

Multi-omics integration
Genomics, transcriptomics, metagenomics, metabolomics, epigenomics and proteomics — all in one subject profile.
Ontology-guided form builder
Build custom CRFs with real-time HPO and SNOMED CT suggestions. Semantic annotation happens at design time, not after.
nf-core pipeline import
One-click import of sarek, rnaseq and megSAP outputs. Pipeline version and parameters recorded for full reproducibility.
Data sovereignty by design
Raw files stay on your Nextcloud. GDPR-compliant. Embargo-ready — FAIR does not mean open.
Integrated biobanking
Five-level biobank hierarchy natively integrated. From container to sample, linked directly to subject profiles and experiments.
Role-based access control
Granular RBAC per user, project and data type. Inherits institutional LDAP and Shibboleth authentication.
Longitudinal data management
Generalized visit model supports clinical visits, questionnaire sessions, experimental timepoints and non-clinical contexts uniformly.
Atomic database design
Every concept decomposed to its smallest SQL-representable unit. Optimized indexes, typed variables, maximum query performance.
Genealogy and household
Relational family trees and household structures built in. Essential for rare disease genetics and microbiome family studies.
Database architecture
Knowledge database
co-shared
84
tables · Ontologies, taxonomies, gene models, metabolites, variants, pipelines. Pre-loaded at every Docker deployment. No personal data.
Research data database
shared
80
tables · Subjects, visits, samples, omics, biobanking, families, households. Empty at deployment. Atomic design for maximum query performance.
Deployments

Operational in real-world research

SHaReD is not a prototype. It runs in production across multiple translational research programs in Germany and Europe. SHaReD — originally the "Shared Hannover RESIST Database" — was first built for the RESIST Excellence Cluster at Medizinische Hochschule Hannover (MHH), and has since evolved into a general-purpose infrastructure adopted across independent programs.

Active
RESIST Excellence Cluster
Multi-institutional translational research program integrating clinical phenotyping, functional immunology and multi-omics. 10+ active cohorts, hundreds of multi-layered subject profiles across independent laboratories.
In adoption
MoreHealth Lower Saxony
€3M project funded by the Lower Saxony Ministry of Science. MHH, UMG Göttingen, TU Braunschweig and Helmholtz HZI. SHaReD as the standardization and quality control infrastructure for multi-omics data across Lower Saxony.
In adoption
Immune-AI — ERDERA JTC 2025
European transnational consortium for rare disease preclinical therapy research. SHaReD as the pre-AI data management infrastructure, ensuring semantically consistent and reproducible input for AI models across partner institutions.
In adoption
Proietti_Lab
Immunology research group at Hannover Medical School (MHH) and the University of Freiburg, combining experimental and computational approaches to genetic immune regulation. SHaReD as the FAIR data management backbone for genetic and multi-omics datasets underlying the lab's immune disorder research.
In adoption
Grimbacher_Lab
Research group at the Center for Chronic Immunodeficiency (CCI), Medical Center – University of Freiburg, investigating the genetic causes of inborn errors of immunity through genomics, epigenetics and metagenomics.

Ready to make your data FAIR from day one?

SHaReD deploys as a Docker appliance. Full documentation, configuration guides and dummy data schemas are available on GitHub.

View on GitHub Documentation Contact the team