dbsnp-database

1# dbSNP Database Integration
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/dbsnp_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 https://www.ncbi.nlm.nih.gov/snp/, then (2)
10    create the file recording the notification text and timestamp.
113.  **`.env` file**: Make sure the `.env` file exists in your home directory.
12    Create one if it does not exist.
134.  **`NCBI_API_KEY`** (optional): Raises the NCBI rate limit from 3 to 10
14    requests/second. The skill works without it, but a key is recommended if the
15    user plans many queries or encounters a 429 error. You can register for a
16    key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You **MUST**
17    use the safe credentials protocol in the `credentials` skill to check for
18    and request this key if this skill looks relevant to the user's request.
19 
20## Core Rules
21 
22-   **Use the Wrapper**: ALWAYS execute the provided wrapper script
23    `scripts/dbsnp_cli.py` to query the database rather than constructing custom
24    HTTP or curl requests. The script automatically handles rate limiting,
25    retries, and JSON parsing.
26-   **Command Choice**: Do NOT use `search-region` to find the rsID of a
27    specific variant; use `resolve-variant` instead.
28…