gget (Claude Skill)

Claude skill that teaches the gget unified API for querying 20+ genomics databases from a single Python or command-line interface.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — actively maintained 2025–2026
Pricing Free / OSS
Capabilities Read-only — queries public databases via gget
Verified works · 2026-07-20
Security cleared · 2026-07-20 — provenance matches K-Dense-AI, MIT repo, maintained, no OSV advisories

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/genomics-bioinformatics/databases/gget-genomic-databases into ~/.claude/skills/).
  • Also available as an MCP server (longevity-genie/gget-mcp, MIT, PyPI gget-mcp) — exposes gget’s functions as discrete MCP tools rather than as a skill; no API key. Register with Claude Code (stdio — Claude Code launches the process itself, so don’t run it separately): 
    claude mcp add --transport stdio gget-mcp -- uvx --from gget-mcp@latest stdio

    Or with Claude Desktop, add to claude_desktop_config.json:

    {
  "mcpServers": {
    "gget-mcp": { "command": "uvx", "args": ["--from", "gget-mcp@latest", "stdio"] }
  }
}

    (Requires uv; use uvx --from gget-mcp@latest server instead of stdio for streamable-HTTP transport.)

  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the gget skill when prompted (also works in Cursor/Codex via the Agent Skills spec; requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/gget ~/.claude/skills/
pip install gget

What it does

Recipes for gget commands against:

  • Ensembl — gene information, sequences, orthologs, variants
  • UniProt — protein sequences and annotations
  • NCBI — BLAST searches, gene information
  • RCSB PDB — protein structures
  • COSMIC — cancer mutations
  • Other curated databases through a single Python/CLI interface

Includes batch-query support, pandas DataFrame integration, and result formatting.

Primary use cases: Quick gene lookups, sequence retrieval, variant annotation, orthology checks, protein structure access without per-database API setup.

Notes

Useful when a workflow needs heterogeneous lookups (gene → sequence → ortholog → structure) without orchestrating separate database clients. For dedicated UniProt or PDB workflows, the standalone MCP servers expose more specialised tooling.

Two packagings of the same underlying gget library are offered above: the K-Dense/SciAgent skills (procedural recipes Claude follows in local Python) and the longevity-genie/gget-mcp MCP server (gget functions exposed as discrete tools — gget_search, gget_info, gget_seq, gget_ref, gget_blast, gget_blat, gget_muscle, gget_archs4, gget_enrichr, gget_pdb, gget_alphafold, gget_cosmic, gget_cellxgene). Pick the MCP path if you want Claude to call gget mid-conversation; pick a skill if you prefer scripted, reproducible runs.

Sources

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