Lamindb

---
name: lamindb
description: Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.
license: Apache-2.0 license
metadata: {"version": "1.1", "skill-author": "K-Dense Inc."}
---

# LaminDB

## Overview

LaminDB is an open-source, lineage-native lakehouse for biology. It makes datasets and models queryable, traceable, validated, reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable) while storing data in open formats across local filesystems, S3, GCS, Hugging Face, SQLite, and Postgres.

**Core Value Proposition:**
- **Queryability**: Search and filter artifacts, records, runs, features, schemas, and collections
- **Traceability**: Track inputs, outputs, parameters, source code, and environments for notebooks, scripts, functions, and pipelines
- **Validation**: Curate DataFrame, AnnData, SpatialData, TileDB-SOMA, Parquet, Zarr, and other biological formats with schemas
- **FAIR Compliance**: Standardize annotations with Bionty-backed ontologies and custom registries
- **Change management**: Organize work with projects, branches, spaces, collections, and saved notes or plans

## 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… load the full skill through Skill Me