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LaminDB Biological Data Curation

Register, validate, annotate and track biological datasets with LaminDB metadata and lineage

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
8 files

What it does

This skill teaches an AI agent how to manage biological datasets using LaminDB, an open-source data management tool. Once installed, the agent follows a defined workflow: it defines typed metadata features and schemas, validates tables and AnnData objects against them, standardizes terms using Bionty ontologies, saves files as tracked artifacts, and records which scripts produced which outputs. It also knows specific pitfalls in the LaminDB 2.10.0 API to avoid. Validation checks structure and types only; it does not judge whether scientific values are correct.

Great for

  • Bioinformatics or lab data teams who want reproducible, traceable dataset curation
  • Developers building a LaminDB lakehouse or metadata pipeline for biological data
  • Students learning how structured metadata and provenance work in research data

Skip it if

  • Projects needing only general-purpose data cleaning with no biological metadata or provenance requirements, since the setup overhead is high
  • Users expecting automatic scientific QC or FAIR compliance; the skill itself states registration does not establish validity, so assay-specific checks must be added by hand
  • Work on production instances with write access without review, because the skill runs scripts that create and save records to the configured storage

Try asking

  • “Set up a local LaminDB instance with the bionty module and save a QC metadata table as a validated artifact”
  • “Define features and a schema that rejects extra columns, then validate a pandas DataFrame against it”
  • “Standardize condition or organism labels against Bionty ontologies and report unresolved values”
  • “Trace which script and input artifacts produced a saved output dataset”
Step-by-step guide: how to use LaminDB Biological Data CurationInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 8 original files, the MIT licence and an attribution note.

    lamindb.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip lamindb.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip lamindb.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Use a new empty project directory and a dedicated virtual environment for experiments, as the skill recommends, to avoid writing to a shared instance.
  • Run lamin info first to confirm which instance and storage the agent will write to before any save.
  • Record artifact UIDs and schema versions for reproducibility, since keys can later resolve to newer versions.

What's inside

  • 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
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.