db-chembl

Goal

To programmatically query the ChEMBL database web services and retrieve reproducible, model-ready datasets of targets, molecules, and bioactivities, while preserving provenance (assay/document IDs) and enabling common curation filters (e.g., pChEMBL, standardized units, handling censoring operators, assay type).

ChEMBL activity data is curated and standardized, but downstream modeling still requires careful selection/filters to avoid mixing incompatible assay formats or censored measurements.

Instructions

1. Search for candidate targets by name (broad recall)

Use this when you only have a gene/protein string and want candidate ChEMBL target IDs.

# Env: base-agent
python .agents/skills/drug-db-chembl/scripts/query_chembl.py \
  --target "EGFR" \
  --max_results 20 \
  --output egfr_targets.json