Description
lamindb is an agent skill for managing biological datasets and models with LaminDB. It covers registering artefacts, curating DataFrame and AnnData metadata, querying annotated artefacts, tracking lineage for scientific scripts and workflows, validating schemas, and annotating with Bionty ontologies. LaminDB keeps metadata in SQLite or PostgreSQL, and keeps the files in configured storage. The skill is clear that registration alone does not establish scientific validity or FAIR compliance. It targets LaminDB 2.10.0 and Bionty 2.5.0. The local examples were run on Python 3.12 with pandas 3.0.6 and AnnData 0.13.2, and the skill notes that this LaminDB release caps AnnData at 0.13.2, so the dependency constraints must be kept. It also says to install IPython for the registry synonym helpers, because one of them imports it in this release. Use it when you want a reproducible record of which dataset, model or script produced which result, with metadata that other people can query. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…
Highlights
- Artefact registration with lineage tracking
- DataFrame and AnnData metadata curation
- Schema validation
- Bionty ontology annotation
- Targets LaminDB 2.10.0 and Bionty 2.5.0
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lamindb FAQ
What is LaminDB used for?
Registering biological datasets and models, tracking which scripts produced them, and querying annotated artefacts.
Where is the metadata stored?
In SQLite or PostgreSQL. Files are kept in the storage you configure.
Does registering data make it FAIR?
No. The skill says registration alone does not establish scientific validity or FAIR compliance.
Which versions does it target?
LaminDB 2.10.0 and Bionty 2.5.0, tested on Python 3.12 with AnnData 0.13.2, which this release caps.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill lamindb.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best lamindb alternatives?
Popular alternatives to lamindb include gget, ai-research-explore and ai-research-reproduction. See all lamindb alternatives