Building trustworthy computational infrastructure for biomedical discovery.
Open-source biomedical informatics infrastructure for interoperable genomic, phenotypic, clinical, and AI-enabled research.
We are a biomedical informatics research and software engineering initiative affiliated with the Biomedical Genomics Group at CNAG.
We develop open-source computational infrastructure that enables researchers to work with complex genomic, phenotypic, and clinical data. Our work spans biomedical interoperability, reproducible analysis, semantic technologies, and trustworthy AI, with the goal of making biomedical discovery more accessible, reproducible, and scalable.
Rather than building isolated applications, we develop reusable infrastructure that connects data, standards, analytical workflows, and AI into a coherent research ecosystem.
Our mission is simple:
Build computational infrastructure that enables biomedical discoveries.
We focus on:
- 🔄 Biomedical data interoperability
- 🧬 Translational informatics
- 🤖 Trustworthy AI for biomedical research
- 🏗️ Sustainable open infrastructure
- 📊 Reproducible computational workflows
We build practical software that helps researchers and clinicians spend less time integrating data and more time answering biological and clinical questions.
Our work is shaped by more than two decades of experience in computational biology and bioinformatics across evolving sequencing technologies, biomedical standards, and computational systems.
We prioritize:
- 🔄 Interoperability over isolated silos
- 🧪 Reproducibility through reusable workflows
- 🏗️ Sustainable infrastructure instead of short-lived prototypes
- 📚 Open science and accessible software
- 🤖 Pragmatic, trustworthy AI grounded in structured biomedical data
We believe the future of biomedical AI depends on reliable infrastructure, interoperable standards, transparent data models, and sustainable software ecosystems.
Our software ecosystem is modular by design. Each project solves a specific problem while contributing to a unified biomedical research platform.
Interconversion between biomedical and phenotypic data standards.
- Phenopackets interoperability
- REDCap, OMOP-CDM and CDISC-ODM support
- CLI, API and Web UI
- Dockerized deployment
Resources
- https://github.com/CNAG-Biomedical-Informatics/convert-pheno
- https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui
- https://cnag-biomedical-informatics.github.io/convert-pheno
GA4GH Beacon v2 interoperability, validation and ingestion tooling.
Resources
Validation workflows for OMOP-CDM CSV datasets.
Resources
Semantic comparison and ranking of interoperable phenotypic data.
- Semantic similarity workflows
- Cross-format interoperability
- Interactive Web UI
Resources
- https://github.com/CNAG-Biomedical-Informatics/pheno-ranker
- https://github.com/CNAG-Biomedical-Informatics/pheno-ranker-ui
- https://cnag-biomedical-informatics.github.io/pheno-ranker
Schema-driven biomedical identifier generation and validation.
Resources
- https://github.com/CNAG-Biomedical-Informatics/clarid-tools
- https://cnag-biomedical-informatics.github.io/clarid-tools
Configuration-driven genomic variant-calling workflows.
Resources
A secure AI-enabled research platform integrating multimodal biomedical data, semantic interoperability, reusable analytical workflows, local and cloud LLMs, and the broader CNAG Biomedical Informatics ecosystem.
The Navigator is designed to become the integration layer for our software ecosystem rather than another standalone application.
- GA4GH Beacon v2
- GA4GH Phenopackets
- OMOP-CDM
- REDCap
- CDISC-ODM
- openEHR
- JSON Schema
- Python
- Perl
- JavaScript / React
- R
- Docker
- MongoDB
- Snakemake
- REST APIs
- Local LLMs
- MCP-compatible workflows
We actively collaborate within the ELIXIR community and participate in European initiatives focused on interoperable biomedical data, federated analytics, translational informatics, and precision medicine.
https://hereditary-project.eu/
Foundation cohort for our long-term work on AI-assisted biomedical research infrastructure for immune-mediated diseases.
https://doi.org/10.1186/s13326-026-00349-6
https://doi.org/10.1093/bioinformatics/btac568
https://doi.org/10.1101/2024.12.25.24319606
https://doi.org/10.1016/j.jbi.2023.104558
https://doi.org/10.1186/s12859-024-05993-2
We are building more than individual software tools.
Our long-term goal is to create an open, modular research platform where interoperable biomedical data, computational methods, and trustworthy AI work together to accelerate biomedical discovery.
If our software enables researchers to answer questions they could not answer before, then we have achieved our goal.
We welcome:
- Scientific collaborations
- Interoperability initiatives
- Standards-related projects
- Open-source contributions
- Bug reports and feature requests
- https://github.com/CNAG-Biomedical-Informatics
- https://cnag-biomedical-informatics.github.io/convert-pheno
- https://cnag-biomedical-informatics.github.io/pheno-ranker
- https://cnag-biomedical-informatics.github.io/clarid-tools
Building sustainable biomedical informatics infrastructure for interoperable and AI-assisted research.
