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Use when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls for human genomic variants.
Passed 8 of 14 test cases with the skill, and 4 of 14 without it.
and 5 more in the full report
8 fixed4 passed either way8 still failing2 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 8 test cases the skill fixed. Same model, same prompt, with and without the skill.
Before making queries in a fresh project folder where LICENSE_NOTIFICATION.txt does not exist, what mandatory step must be taken regarding terms?
| Checked | Without skill | With skill |
|---|---|---|
| Notifies user about NCBI ClinVar terms and creates LICENSE_NOTIFICATION.txt with timestamp | Missed | Passed |
The instructions your model reads when the skill loads.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.ncbi.nlm.nih.gov/clinvar/, then (2) create the file recording the notification text and timestamp.
.env file: Make sure the .env file exists in your home directory.
Create one if it does not exist.
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. The user can obtain one
for free by registering at https://www.ncbi.nlm.nih.gov/account/settings/.
If the variable is missing from .env, do NOT ask the user to paste it into
the chat (this would leak the key into the agent's context). Instead, give
the user this command — substituting ENV_FILE with the resolved literal
path to the .env file:
printf "Enter NCBI API key (typing hidden): " && read -s key && echo && echo "NCBI_API_KEY=$key" >> "ENV_FILE" && echo "Saved."
The scripts load credentials automatically via dotenv. NEVER read,
print, or inspect the .env file or its variables (e.g. no cat, grep,
echo, printenv, or os.environ.get on keys). Credentials must stay out
of the agent's context. See the
API Key section for more details.
ClinVar is the primary consensus record for clinical classifications of human genomic variations. It provides the "clinical ground truth" for pathogenicity labels (Pathogenic, Likely Pathogenic, Benign, VUS) based on assertions from global laboratories.
test cases passed, vs 4 / 14 without
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