| 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.
