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ncbi-entrez-skill — Codex skill: what it does, how to install

This skill sends NCBI Entrez requests for PubMed, Gene, Protein, Nucleotide, PMC, and GEO data. Use it for focused search and record lookups.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill ncbi-entrez-skill -a codex
Open on GitHub

What ncbi-entrez-skill does

ncbi-entrez-skill sends NCBI Entrez E-Utilities requests through scripts/ncbi_entrez.py. It supports esearch, esummary, efetch, elink, and einfo, with PubMed, Gene, Protein, Nucleotide, and PMC databases. GEO requests use gds or geoprofiles.

The default output is a concise markdown summary, a compact record set, or the start of the response. Request save_raw=true when you need the full JSON or XML, then use raw_output_path for the saved file location. PMID and DOI values are rendered as links in user-facing results.

Install it when an agent needs targeted Entrez searches, summaries, record fetches, or cross-database links. BLAST, PMC Open Access, and NCBI Datasets v2 workflows belong to separate skills.

What it helps with

  • search PubMed for a research query
  • retrieve gene and protein summaries
  • fetch Nucleotide or Protein records
  • query GEO metadata
  • link records across NCBI databases

Example prompts for the agent

  • Search PubMed for `KRAS AND colorectal cancer` and return a concise summary.
  • Use `esummary` to retrieve the Gene record for `7157`.
  • Use `elink` to find PubMed links for a GEO record.

How to install ncbi-entrez-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill ncbi-entrez-skill -a codex

2Manually: put the files in place

.agents/skills/ncbi-entrez-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about ncbi-entrez-skill

How do I install ncbi-entrez-skill in Codex?

Run npx skills add openai/plugins --skill ncbi-entrez-skill. The skill file is then available at .agents/skills/ncbi-entrez-skill/SKILL.md.

What does ncbi-entrez-skill do?

It sends compact NCBI Entrez E-Utilities requests for searches, summaries, record fetches, and links between databases.

Can it return full JSON or XML?

Yes. Ask for save_raw=true and set raw_output_path when the raw response needs to be saved at a specific path.

See also

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