lamindb

Topics in the source

• LaminDB
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Core Concepts and Data Lineage
• 2. Data Management and Querying
• 3. Annotation and Validation
• 4. Biological Ontologies

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 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 da

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