Building trustworthy computational infrastructure for biomedical discovery.
CNAG Biomedical Informatics is a research software laboratory within CNAG's Biomedical Genomics Group. We develop open-source infrastructure that connects genomic, phenotypic, clinical, and imaging data with reproducible analysis and trustworthy AI.
Each project addresses a focused research need while contributing to a shared, standards-based software ecosystem. Project names link to their documentation.
- Beacon v2 CBI Tools validates and ingests data for GA4GH Beacon v2.
- CBIcall runs configuration-driven genomic variant-calling workflows.
- Convert-Pheno interconverts biomedical and phenotypic data standards.
- Pheno-Ranker compares and ranks interoperable phenotypic profiles.
- OMOP CSV Validator checks OMOP-CDM CSV datasets before ingestion.
- ClarID-Tools generates and validates schema-driven biomedical identifiers.
- dicomqc audits DICOM metadata de-identification and research-release readiness.
- OmicsDM stores and shares processed omics data with associated pheno-clinical information.
- COHORTome is an open-source workbench for governed longitudinal and multimodal cohort analysis (Technical Note manuscript in preparation for GigaScience).
We use established biomedical standards and transparent data models as shared interfaces across the toolkit. Structured configuration and reusable workflows make analyses inspectable and repeatable, while open development supports long-term maintenance and reuse.
Our work grows through collaboration with the Global Alliance for Genomics and Health (GA4GH), the ELIXIR community, and European research initiatives in interoperable biomedical data, federated analytics, translational informatics, and precision medicine, including 3TR, HEREDITARY, and PRECISESADS.
- ClarID
- Beacon v2 Reference Implementation
- OMOP CDM to Beacon v2 Interoperability
- Convert-Pheno
- Pheno-Ranker
Our goal is practical: help researchers spend less time integrating data and more time answering biological and clinical questions.
