epigraphdb-skill

name: epigraphdb-skill description: Submit compact EpiGraphDB API requests for ontology, literature, MR, gene-drug, and support-path evidence. Use when a user wants concise EpiGraphDB summaries

Operating rules

• Use scripts/rest_request.py for all EpiGraphDB API calls.
• Use base_url=https://api.epigraphdb.org.
• Start with max_items=10 for list-style endpoints; use smaller caps for literature-heavy or pairwise endpoints if the response fans out quickly.
• Prefer the connectivity guard endpoints first when endpoint availability matters: ping, builds, and meta/api-endpoints.
• Re-run requests in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Prefer targeted paths such as ontology/gwas-efo, gene/drugs, gene/druggability/ppi, mr, and literature/gwas.
• If the user needs the full payload, set save_raw=true and report the saved file path.

Input

• Read one JSON object from stdin.
• Required fields: base_url, path
• Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common EpiGraphDB patterns:
  • {"base_url":"https://api.epigraphdb.org","path":"ping"}
  • {"base_url":"https://api.epigraphdb.org","path":"ontology/gwas-efo","params":{"trait":"asthma","score_threshold":0.8,"fuzzy":true},"max_items":10}
  • {"base_url":"https://api.epigraphdb.org","path":"gene/drugs","params":{"gene_name":"IL6R"},"max_items":10}

Output

• Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://api.epigraphdb.org","path":"ontology/gwas-efo","params":{"trait":"asthma","score_threshold":0.8,"fuzzy":true},"max_items":10}' | python scripts/rest_request.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.