lamindb

Track biological data lineage with ontology-aware annotations via Bionty.

1|Updated Mar 4, 2026
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill lamindb-hung-3008
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: lamindb
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/lamindb
Command: npx skills add https://github.com/Hung-3008/agusta --skill lamindb-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

LaminDB resolves the challenge of organizing, validating, and reproducing complex biological data by providing end-to-end lineage tracking and ontology-aware metadata management.

Core Features & Use Cases

  • Ontology-driven curation and annotation of biological datasets (cell types, tissues, diseases)
  • Full data lineage tracking across artifacts, runs, and transforms
  • Schema-based validation and standardization to ensure reproducibility

Quick Start

Start tracking with LaminDB and load a dataset to begin ontology-enabled curation.

Frequently Asked Questions about lamindb

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I track data lineage and reproduce scRNA-seq analysis runs?

Track scRNA-seq data lineage by linking artifacts, runs, and transforms to create traceable workflows. This schema-based validation ensures biological data analysis is fully reproducible and auditable across multi-omics experiments.

What is ontology-aware annotation for biological data management?

Ontology-aware annotation standardizes biological metadata by mapping cell types, tissues, and diseases to controlled vocabularies via Bionty. This validation ensures datasets remain consistent, searchable, and interoperable across complex multi-omics workflows.

Can I use LaminDB for curating spatial transcriptomics and flow cytometry datasets?

LaminDB supports spatial transcriptomics, flow cytometry, and scRNA-seq workflows for data curation. You can apply ontology-driven annotation and track full data lineage across these diverse biological data modalities to ensure reproducible research.

How does biological data lineage tracking compare to general data management?

Biological data lineage tracking captures experiment-specific transforms and runs, whereas general data management only stores files. This approach provides end-to-end provenance and ontology-aware validation specifically for complex multi-omics workflows.

Does LaminDB integrate with existing workflow tools for multi-omics data validation?

LaminDB offers flexible deployment options and workflow tool integrations for multi-omics data validation. It connects your existing pipeline transforms to tracked artifacts, maintaining complete provenance without disrupting your established analysis environment.

When should I use schema-based validation for biological datasets?

Use schema-based validation when standardizing complex biological datasets to ensure reproducibility. It enforces ontology-aware metadata structures across artifacts and transforms, preventing annotation errors before they propagate through downstream analysis.