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epigraphdb-skill

Query the EpiGraphDB API for ontology, literature, MR, and gene-drug evidence summaries.

5.3k|765|Updated Mar 4, 2026
Search Tags:#api#biomedical#gwas#reST#gene-drug#mendelian randomization#epigraphdb
One-click install
npx skills add https://github.com/openai/plugins --skill epigraphdb-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: epigraphdb-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/epigraphdb-skill
Command: npx skills add https://github.com/openai/plugins --skill epigraphdb-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers need quick, compact access to EpiGraphDB's biomedical knowledge graph without writing custom API clients or parsing large raw JSON payloads by hand.

Core Features & Use Cases

  • Compact API Requests: Submit GET/POST requests to any EpiGraphDB endpoint with automatic response compaction, record extraction, and truncation controls.
  • Targeted Evidence Paths: Query ontology mappings (gwas-efo), gene-drug relationships, druggability PPI, Mendelian randomization, and literature endpoints with sensible defaults.
  • Raw Payload Export: Save full JSON responses to disk when complete data is needed for downstream analysis.
  • Use Case: Ask for drug targets associated with IL6R, and receive a concise markdown summary of gene-drug evidence capped at 10 records instead of a massive raw response.

Quick Start

Ask the assistant to fetch EpiGraphDB ontology mappings for asthma with a score threshold of 0.8 and summarize the top results.

Frequently Asked Questions about epigraphdb-skill

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

FAQPage Schema
How do I query the EpiGraphDB API for gene-drug associations?▼

Send a JSON request with path gene/drugs and a params object containing the gene name, such as IL6R. The script returns up to max_items compact records summarizing the drug evidence for that gene.

How do I get GWAS ontology mappings for a trait from EpiGraphDB?▼

Use the ontology/gwas-efo path with params including the trait name, a score_threshold, and fuzzy matching. For example, query asthma with score_threshold 0.8 to retrieve EFO ontology mappings capped by max_items.

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

Yes, set save_raw to true in the input JSON and optionally specify raw_output_path. The full response is written to disk and the returned output includes the saved file path.

What Python dependencies does the EpiGraphDB request script need?▼

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

Why does the EpiGraphDB response show truncated records?▼

Responses are compacted by default using max_items and max_depth limits to keep output concise. Increase max_items or set save_raw to true when you need the complete payload.

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