ChEMBL Database Query

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
2. User Notification: If .licenses/chembl_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://chembl.gitbook.io/chembl-interface-documentation/about, then (2) create the file recording the notification text and timestamp.

Core Rules

• [!IMPORTANT] Use the Utility Scripts: You MUST ALWAYS use the provided utility script scripts/chembl_api.py for all ChEMBL API interactions, including checking status. NEVER use curl or custom Python requests to query the ChEMBL API directly. This ensures rate limit is enfoced and also retries on network errors.

• Output to File (Required): The --output flag is required for every subcommand. All JSON results are written to the specified file. After running the command, read the output file with jq or your own code to extract the data. List results are typically wrapped in a JSON array keyed by the endpoint name (e.g., molecules, activities).

• Notification: If this skill is used, ensure this is mentioned in the output.

Utility Script

All ChEMBL API queries use one script with subcommands:

uv run scripts/chembl_api.py <subcommand> --output <file> [options]

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1. Check API Status

uv run scripts/chembl_api.py status --output /tmp/status.json

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2. Molecule Queries

Fetch by ChEMBL ID: bash uv run scripts/chembl_api.py molecule --id CHEMBL25 --output /tmp/mol.json

Search by name: bash uv run scripts/chembl_api.py molecule --search "aspirin" --limit 3 --output /tmp/mol_search.json