alterlab-lamindb

# LaminDB ## Overview LaminDB is an open-source data framework for biology designed to make data queryable, traceable, reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable). It provides a unified platform that combines lakehouse architecture, lineage tracking, feature stores, biological ontologies, LIMS (Laboratory Information Management System), and ELN (Electronic Lab Notebook) capabilities through a single Python API. **Core Value Proposition:** - **Queryability**: Search and filter datasets by metadata, features, and ontology terms - **Traceability**: Automatic lineage tracking from raw data through analysis to results - **Reproducibility**: Version control for data, code, and environment - **FAIR Compliance**: Standardized annotations using biological ontologies ## When to Use This Skill Use this skill when: - **Managing biological datasets**: scRNA-seq, bulk RNA-seq, spatial transcriptomics, flow cytometry, multi-modal data, EHR data - **Tracking computational workflows**: Notebooks, scripts, pipeline execution (Nextflow, Snakemake, Redun) - **Curating and validating data**: Schema validation, standardization, ontology-based annotation - **Working with biological ontologies**: Genes, proteins, cell types, tissues, diseases, pathways (via Bionty) - **Building data lakehouses**: Unified query interface across multiple datasets - **Ensuring reproducibility**: Automatic versioning, lineage tracking, environment capture - **Integrating ML pipelines**: ...