clinvar-database

1# ClinVar 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/clinvar_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/clinvar/, then
10    (2) 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## Overview
21 
22ClinVar is the primary consensus record for clinical classifications of human
23genomic variations. It provides the "clinical ground truth" for pathogenicity
24labels (Pathogenic, Likely Pathogenic, Benign, VUS) based on assertions from
25global laboratories.
26 
27## When to Use
28 
29**Use when you need to:**
30 
31-   Find the current clinical significance and star rating (review status) for a
32    specific variant.
33…