dbSNP Database Integration

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/dbsnp_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ncbi.nlm.nih.gov/snp/, then (2) create the file recording the notification text and timestamp.
3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist.
4. NCBI_API_KEY (optional): Raises the NCBI rate limit from 3 to 10 requests/second. The skill works without it, but a key is recommended if the user plans many queries or encounters a 429 error. You can register for a key for free at https://www.ncbi.nlm.nih.gov/account/settings/. You MUST use the safe credentials protocol in the credentials skill to check for and request this key if this skill looks relevant to the user's request.

Core Rules

• Use the Wrapper: ALWAYS execute the provided wrapper script scripts/dbsnp_cli.py to query the database rather than constructing custom HTTP or curl requests. The script automatically handles rate limiting, retries, and JSON parsing.
• Command Choice: Do NOT use search-region to find the rsID of a specific variant; use resolve-variant instead.
• Output Size: Avoid using --full on get-variant unless specifically needed, as raw payloads can exceed 1 MB.
• Shell Safety: Always wrap HGVS strings in single quotes to prevent shell expansion errors.
• Notification: If this skill is used, ensure this is mentioned in the output.

When to Use

Use this skill when you need to: