Lamindb

What it does

When your agent uses it

• Reproducible biological data curation
• A LaminDB lakehouse

Example prompts

• “Use the lamindb skill to manage biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation…”
• “/lamindb”

Requirements

• Python 3
• Compatibility (from SKILL.md): Requires Python 3.10-3.14 and lamindb; examples tested on Python 3.12 with lamindb 2.10.0, bionty 2.5.0, and IPython. Local SQLite needs no login; public ontologies and remote storage require network access, and private instances require credentials.

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Confirm the intended instance, storage, and write scope with lamin info.
2. 2Define typed Feature records and a Schema for the biological data.
3. 3Review the ontology source/version and organism. Standardize only reviewed
4. 4In a script or notebook, start ln.track(), load registered inputs, validate,
5. 5Save through the curator or a schema-aware artifact constructor. Check the
6. 6Query metadata before loading content. Record artifact UIDs and schema/source

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • uv
  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • arxiv.org
  • doi.org
  • export.arxiv.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires Python 3.10-3.14 and lamindb; examples tested on Python 3.12 with lamindb 2.10.0, bionty 2.5.0, and IPython. Local SQLite needs no login; public ontologies and remote storage require network access, and private instances require credentials.

  From compatibility in the SKILL.md frontmatter.

Context cost

Lamindb loads about 2.1k tokens when it runs, and up to ~12k if it reads all its reference files. Until then it costs about 75 tokens; SKILL.md has 808 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~75

When it runs · the whole SKILL.md, loaded when a task matches

~2.1k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~12k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its Apache-2.0 licence (© K-Dense-AI). 808 words, ~2,051 tokens.

name

lamindb

description

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage, and workflow integrations. Use for reproducible biological data curation or a LaminDB lakehouse.

compatibility

Requires Python 3.10-3.14 and lamindb; examples tested on Python 3.12 with lamindb 2.10.0, bionty 2.5.0, and IPython. Local SQLite needs no login; public ontologies and remote storage require network access, and private instances require credentials.

license

Apache-2.0 license

metadata.version

2.0

metadata.last-reviewed

2026-09-30

metadata.skill-author

K-Dense Inc.

uv venv --python 3.12
uv pip install 'lamindb==2.10.0' 'bionty==2.5.0' 'ipython==9.17.1'
source .venv/bin/activate
lamin init --storage ./storage --name biology-demo --modules bionty

import pandas as pd
import lamindb as ln

ln.track(params={"analysis": "QC metadata curation"})
count = ln.Feature(name="gene_count", dtype=int).save()
condition = ln.Feature(name="condition", dtype=str).save()
schema = ln.Schema(
    name="qc_metadata",
    features=[count, condition],
    maximal_set=True,  # reject extra columns
).save()
df = pd.DataFrame({
    "gene_count": [120, 130],
    "condition": ["control", "treated"],
})
curator = ln.curators.DataFrameCurator(df, schema)
curator.validate()  # raises on invalid data; do not use as an if condition
artifact = curator.save_artifact(key="experiments/qc.parquet")
assert artifact.schema == schema
pd.testing.assert_frame_equal(artifact.load(), df)
ln.finish()

© K-Dense-AI, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 7 other files (references) in skills/lamindb of K-Dense-AI/scientific-agent-skills.

• SKILL.md
• references/annotation-validation.md
• references/core-concepts.md
• references/data-management.md
• references/integrations.md
• references/ontologies.md
• references/setup-deployment.md
• references/sources.md

Open the folder on GitHubat commit 92ace75

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

• lingxling/awesome-skills-cnclaude-scientific-skills/skills/lamindb