Menu

Individual skill

biopython-entrez

0upvotes

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

scientific-skills/Evidence Insight/biopython-entrez/SKILL.md

Read pinned source

Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
Yes
Repository scan complete
No
Skill scan complete
No
Observed behavior
Instructions only
Last checked
Nov 9, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
2,042
Repository last updated
Sep 17, 2026
License
MIT

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt
> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to search PubMed for articles by keyword, author, journal, or date range and then retrieve metadata or abstracts.
- You want to download GenBank records (e.g., nucleotide/protein sequences) in batch given accession IDs or search queries.
- You need to convert identifiers or discover related records across NCBI databases (e.g., PubMed ↔ PMC, Gene ↔ Protein) via cross-links.
- You must retrieve lightweight summaries (titles, IDs, basic metadata) before deciding which full records to fetch.
- You are integrating NCBI E-utilities into an automated pipeline and need API key usage and rate-limit-aware requests.

## Key Features

- Supports core NCBI E-utilities via `Bio.Entrez`: `esearch`, `efetch`, `esummary`, `elink`.
- Query-based searching and ID list retrieval for downstream batch operations.
- Batch downloading of records in common formats (e.g., GenBank, FASTA, XML).
Back to top