Bioactivity and Assay Data Retrieval

Goal

To programmatically retrieve the testing history of a specific chemical compound against biological targets using PubChem's Assay Summary endpoint. This skill allows filtering for "Active" outcomes, providing assay IDs (AIDs), target GeneIDs, and micromolar activity values to assess a compound's promiscuity or target specificity.

Instructions

1. Extract All Assays

Retrieve all assays for a given compound (CID), regardless of outcome:

# Env: base-agent
python .agents/skills/drug-bioactivity-assay/scripts/get_assays.py \
  --cid 2244 \
  --limit 50 \
  --outdir research/aspirin_assays \
  --output aspirin_all_assays.json