| name | hmdb-skill |
| description | Submit compact HMDB search requests for metabolites, proteins, diseases, and pathways. Use when a user wants concise HMDB summaries |
Operating rules
- Use
scripts/rest_request.py for all HMDB calls.
- Use
base_url=https://hmdb.ca.
- Search endpoints are better with
per_page=10 and max_items=10.
- Keep category-specific requests narrow instead of broad searches across multiple categories at once.
- 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
unearth/q with explicit query, category, and format=json.
- 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 HMDB patterns:
{"base_url":"https://hmdb.ca","path":"unearth/q","params":{"query":"serotonin","category":"metabolites","format":"json","per_page":10},"record_path":"metabolites","max_items":10}{"base_url":"https://hmdb.ca","path":"unearth/q","params":{"query":"glycolysis","category":"pathways","format":"json","per_page":10},"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://hmdb.ca","path":"unearth/q","params":{"query":"serotonin","category":"metabolites","format":"json","per_page":10},"record_path":"metabolites","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.
