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bioservices — Claude Code skill: what it does, how to install

Guides Python workflows using BioServices to query biological databases. Useful for mapping protein IDs, extracting KEGG pathways, and resolving chemical identifiers.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices -a claude-code
Open on GitHub

What bioservices does

This skill guides the agent in using the bioservices package (version 1.16.0) in Python scripts. It sets operational patterns for services such as UniProt, KEGG, UniChem, and QuickGO. Each provider has distinct response formats and edge cases. For instance, KEGG requires capping requests at three per second, and its organism listing endpoint returns HTTP 400.

The setup requires Python between 3.9 and 3.13, bioservices==1.16.0, and active network access. If you submit BLAST jobs to EMBL-EBI, provide a contact email through the NCBI_EMAIL environment variable. The library often returns None or an HTTP status code instead of raising an error. This makes explicit return type checks necessary on every request.

What it helps with

  • map protein accessions between UniProt and KEGG
  • parse pathway interaction networks from KGML
  • resolve chemical compound cross-references via UniChem
  • fetch functional gene annotations from QuickGO

Example prompts for the agent

  • Search UniProt for human ZAP70 and return fields as TSV.
  • Fetch pathway hsa04660 from KEGG and parse interactions from the KGML structure.

How to install bioservices

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices -a claude-code

2Manually: put the files in place

~/.claude/skills/bioservices/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/bioservices/

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Questions about bioservices

How to install bioservices in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices -a claude-code in your terminal.

What does bioservices do?

It guides the assistant on querying biological repositories like UniProt, KEGG, QuickGO, and UniChem in Python. It covers query structure, error patterns, and API rate limits.

What are the requirements for bioservices?

You need Python between 3.9 and 3.13 with bioservices==1.16.0 installed, plus network access. Submitting BLAST queries to EMBL-EBI requires setting the NCBI_EMAIL environment variable.

See also

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