skills.rest
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pride-skill

Query the PRIDE Archive API for proteomics project discovery and metadata summaries.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#project discovery#Metadata#proteomics#pride archive#REST api#pxd accession
One-click install
npx skills add https://github.com/openai/plugins --skill pride-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pride-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/pride-skill
Command: npx skills add https://github.com/openai/plugins --skill pride-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers need a quick way to search the PRIDE Archive proteomics repository and retrieve project-level metadata without writing custom API client code or parsing large raw JSON responses.

Core Features & Use Cases

  • Project Discovery: Search PRIDE Archive projects by keyword with controlled page sizes via the projects endpoint.
  • Project Metadata Lookup: Fetch compact metadata for a specific project using its PXD accession (e.g., projects/PXD001357).
  • Compact Output: Returns trimmed JSON records or summaries by default, with optional raw response saving to disk.
  • Use Case: A bioinformatics researcher wants to find recent proteomics datasets on a topic; the skill queries projects with a keyword and returns a concise markdown summary of matching projects.

Quick Start

Ask the assistant to search the PRIDE Archive for proteomics projects matching a keyword and summarize the top results.

Frequently Asked Questions about pride-skill

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

FAQPage Schema
How do I search the PRIDE Archive for proteomics projects?▼

Send a JSON request to the script with base_url set to the PRIDE Archive v2 API, path set to projects, and params containing a keyword and pageSize. The script returns a compact list of matching project records.

How do I get metadata for a specific PRIDE project by PXD accession?▼

Set the path field to projects/<PXD accession>, for example projects/PXD001357, with the PRIDE Archive v2 base URL. The response returns a compact summary of that project's metadata.

What Python dependencies does the PRIDE REST client require?▼

The script requires the requests library for HTTP calls; all other modules come from the Python standard library. If requests is missing, the script returns a missing_dependency error.

Can I save the full raw PRIDE API response to a file?▼

Yes, set save_raw to true and optionally provide raw_output_path in the input JSON. The full response is written to that path, or to a default file under /tmp, while the stdout output stays compact.

What HTTP methods and input formats does the script support?▼

The script supports GET and POST requests, with input provided as a single JSON object on stdin. POST bodies can be sent as json_body or form_body, but not both at once.

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