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Skill v1.0.1
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version: "1.0.1" name: eqtl-catalogue-skill description: Submit compact eQTL Catalogue API requests for association retrieval and documented metadata endpoints. Use when a user wants concise public eQTL Catalogue summaries
Operating rules
- Use
scripts/rest_request.pyfor all eQTL Catalogue calls. - Use
base_url=https://www.ebi.ac.uk/eqtl/api. - Prefer targeted association endpoints over broad list endpoints.
- The public API currently appears strict about query validation, and live smoke tests returned intermittent
400/500/timeout failures even with documented parameter sets; treat this source as usable but upstream-fragile. - For association endpoints, the script now backfills compatibility defaults for
quant_method,p_lower,p_upper, and blank filter strings because the live API is currently rejecting omitted optional filters. - Prefer
variant_idin requests; the script mirrors it to the legacysnpquery key to accommodate the current server-side validator. - Re-run requests in long conversations instead of relying on older tool output.
Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return raw JSON only if the user explicitly asks for machine-readable output.
- Prefer documented association paths such as
genes/<gene_id>/associations,studies/<study>/associations, or tissue/study-scoped association routes with explicit filters, and surface upstream400/500errors verbatim when they occur.
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 eQTL Catalogue patterns:
{"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"genes/ENSG00000141510/associations","params":{"study":"<study>","tissue":"<tissue_ontology_id>","variant_id":"rs7903146","size":10},"max_items":10}{"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"studies/<study>/associations","params":{"tissue":"<tissue_ontology_id>","variant_id":"rs7903146","size":10},"max_items":10}{"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"associations/rs7903146","params":{"size":10},"max_items":10}
Output
- Success returns
ok,source,path,method,status_code,warnings, and either compactrecordsor a compactsummary. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
bash
echo '{"base_url":"https://www.ebi.ac.uk/eqtl/api","path":"genes/ENSG00000141510/associations","params":{"study":"<study>","tissue":"<tissue_ontology_id>","variant_id":"rs7903146","size":10},"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.