pubchem-database

1# PubChem Database
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/pubchem_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://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and
11    https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file
12    recording the notification text and timestamp.
13 
14## Quick Start
15 
16PubChem queries are executed via a robust Python wrapper script to respect
17terms-of-service and handle complex JSON parsing. This script allows safe
18multi-agent use of APIs.
19 
20Example: Resolve a chemical name to its Compound ID (CID)
21 
22```bash
23uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json
24```
25 
26## Core Rules
27 
28-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
29    database rather than accessing the database directly. The scripts
30    automatically enforce the required rate limit gracefully.
31-   Read the generated JSON output file, and process it with jq or code.
32-   **Verify Facts**: ALWAYS verify information retrieved from memory with a
33    database query if the user asks for a specific fact that can be checked in
34    PubChem. Do not rely solely on internal knowledge.
35-   **Notification**: If this skill is used, ensure this is mentioned in the
36    output.
37 
38## Core Capabilities
39…