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biostudies-arrayexpress-skill

Query BioStudies and ArrayExpress APIs for study search and accession retrieval.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#genomics#metadata retrieval#BioStudies#study search#arrayexpress#REST api
One-click install
npx skills add https://github.com/openai/plugins --skill biostudies-arrayexpress-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: biostudies-arrayexpress-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/biostudies-arrayexpress-skill
Command: npx skills add https://github.com/openai/plugins --skill biostudies-arrayexpress-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Researchers often need quick, compact summaries from the BioStudies and ArrayExpress repositories without writing custom API client code or wading through large raw JSON payloads.

Core Features & Use Cases

  • Free-Text Search: Run paginated searches against the BioStudies and ArrayExpress search endpoints with compact, truncated result records.
  • Accession Retrieval: Fetch individual study records by accession (e.g., E-MTAB-6701) via the studies endpoints.
  • Raw Payload Export: Save full JSON responses to disk with save_raw when complete records are needed for downstream analysis.
  • Use Case: A bioinformatician asks for recent single-cell RNA-seq studies; the Skill queries ArrayExpress/search with pageSize=10 and returns a concise markdown summary of matching accessions.

Quick Start

Ask the assistant to search BioStudies for studies matching a keyword such as "rna" and summarize the first ten results.

Frequently Asked Questions about biostudies-arrayexpress-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search BioStudies for studies by keyword?▼

Send a JSON request with path set to search and params containing query, page, and pageSize. The script returns compact records from the hits field, limited by max_items for concise summaries.

How do I retrieve an ArrayExpress study by accession number?▼

Use the studies/<accession> path, for example studies/E-MTAB-6701, with the BioStudies base URL. Accession lookups return a compact summary of the study record and usually do not need max_items.

What Python dependencies does the BioStudies REST client require?▼

The script requires the requests library for HTTP calls; it returns a missing_dependency error if requests is not installed. All other functionality uses the Python standard library.

Can I save the full BioStudies API response instead of a summary?▼

Yes, set save_raw to true in the input JSON and optionally provide raw_output_path. The full JSON payload is written to disk and the output reports the saved file path instead of pasting large records.

Why does the BioStudies search output show truncated fields?▼

The client compacts responses by limiting string length, list items, and nesting depth via max_items and max_depth. Displayed ellipses indicate truncation; increase limits or use save_raw for complete data.

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