LaminDB

About

LaminDB is an open-source data framework designed specifically for the life sciences, transforming complex biological data into queryable, traceable, and FAIR (Findable, Accessible, Interoperable, Reusable) assets. It combines the capabilities of a data lakehouse, lineage tracking system, and biological ontology manager into a single platform, allowing researchers to manage everything from scRNA-seq and spatial transcriptomics to computational workflow tracking. By providing standardized tools for data validation and integration with common MLOps platforms, LaminDB ensures that biological research is reproducible, well-documented, and easily searchable across large-scale datasets.

Key Features

• Automatic lineage tracking for data, code, and execution environments
• Schema validation and standardization for complex biological data types like AnnData and MuData
• Advanced querying and filtering of datasets by metadata, features, and provenance
• Standardized data curation using biological ontologies like genes, cell types, and diseases
• 2,066 GitHub stars
• Integration with workflow managers like Nextflow and Snakemake for pipeline tracking

Use Cases

• Building a queryable and FAIR-compliant data lakehouse for multi-modal biological research
• Tracking end-to-end data lineage from raw sequencing files through analysis notebooks to final results
• Validating and annotating single-cell datasets with standardized ontology terms for better interoperability