chembl-database

1# ChEMBL Database Query
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/chembl_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at
10    https://chembl.gitbook.io/chembl-interface-documentation/about, then (2)
11    create the file recording the notification text and timestamp.
12 
13## Core Rules
14 
15-   [!IMPORTANT] **Use the Utility Scripts**: You MUST ALWAYS use the provided
16    utility script `scripts/chembl_api.py` for all ChEMBL API interactions,
17    including checking status. NEVER use `curl` or custom Python requests to
18    query the ChEMBL API directly. This ensures rate limit is enfoced and also
19    retries on network errors.
20 
21-   **Output to File (Required)**: The `--output` flag is **required** for every
22    subcommand. All JSON results are written to the specified file. After
23    running the command, read the output file with jq or your own code to
24    extract the data. List results are typically wrapped in a JSON array keyed
25    by the endpoint name (e.g., `molecules`, `activities`).
26 
27-   **Notification**: If this skill is used, ensure this is mentioned in the
28    output.
29 
30## Utility Script
31 
32All ChEMBL API queries use one script with subcommands:
33 
34```bash
35uv run scripts/chembl_api.py <subcommand> --output <file> [options]
36```
37…