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Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.
Passed 4 of 9 test cases with the skill, and 4 of 9 without it.
and 3 more in the full report
5 fixed4 passed either way9 still failing5 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
When running scripts/pubmed_api.py to execute fetch_article_abstracts on PMID 35113657, what is the first positional argument passed to the script?
| Checked | Without skill | With skill |
|---|---|---|
| Specifies the output file path as the first positional argument. | 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..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 E-utilities 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/USER_EMAIL (optional but recommended): Identifies the caller to NCBI
(recommended by their Terms of Use).If the variables are missing from .env, do NOT ask the user to paste them into
the chat (this would leak keys into the agent's context). Instead, give the user
these commands — 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=$key" >> "ENV_FILE" && echo "Saved."
printf "Enter contact email: " && read email && echo "USER_EMAIL=$email" >> "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.
test cases passed, vs 4 / 9 without
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