Science Skills is a collection of add-ons that give AI agents structured instructions, scripts, and references for scientific research, including genomics, structural biology, cheminformatics, and literature search. Researchers use it to guide agents through specialized scientific tasks with information from databases and tools such as AlphaGenome, AFDB, and UniProt. The catalogue entries are individual skills from this collection.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/google-deepmind/science-skills/pubmed_databasenpx skills add google-deepmind/science-skills --skill pubmed_databasegit clone --depth 1 https://github.com/google-deepmind/science-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/google-deepmind/science-skills/pubmed_database)<a href="https://agentmods.dev/skills/google-deepmind/science-skills/pubmed_database"><img src="https://agentmods.dev/badge/skills/google-deepmind/science-skills/pubmed_database.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00079 | $0.02007 |
| Opus 5 | $0.00039 | $0.01004 |
| Sonnet 5 | $0.00016 | $0.00401 |
| Haiku 4.5 | $0.00008 | $0.00201 |
Grade A, and why
pubmed-database scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
requests/second. Querying the API any other way (e.g. via curl, wget, or How it starts
The opening of the file, as written. The whole thing — 186 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PubMed API
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/pubmed_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://pubmed.ncbi.nlm.nih.gov/disclaimer/ and https://www.ncbi.nlm.nih.gov/home/about/policies/ and to always check the license of the papers retrieved by the skill for any restrictions, then (2) create the file recording the notification text and timestamp.
.envfile: Make sure the.envfile 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. 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 thecredentialsskill to check for and request this key if this skill looks relevant to the user's request.USER_EMAIL(optional): Identifies the caller to NCBI (recommended by their Terms of Use). You MUST use the safe credentials protocol in thecredentialsskill to check for and request this credential if this skill looks relevant to the user's request.
This skill provides CLI access to the NCBI PubMed and PubMed Central APIs via
scripts/pubmed_api.py — a single CLI with 10 functions covering search, fetch,
linking, full text, spelling, discovery, citation matching, and caching.
Core Rules
- API Use: Always use the provided wrapper
scripts/pubmed_api.pywhich manages rate limits automatically and prevents API abuse. Setting theNCBI_API_KEYenvironment variable raises the rate limit from 3 to 10 requests/second. Querying the API any other way (e.g. via curl, wget, or hand-written code) is strictly forbidden. - JSON Processing: Use
jqto filter and transform JSON output (or python equivalents ifjqis not available) to prevent hallucinations and context overflow. - Temporary Files: To avoid polluting the working directory with JSON
files, use a temporary directory inside the current directory. When running
multiple agents or tasks in parallel, ensure each uses a unique subdirectory
name (e.g.,
tmp_$TASK_ID/) to avoid file collisions. - Notification: If this skill is used, ensure this is mentioned in the output AND list the URLs of all papers that were used in producing the output.
What ships with it
10 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- references/advanced-linking.md 5.4 KB
- references/advanced-search.md 3.6 KB
- references/bulk-workflows.md 3.5 KB
- references/citation-matching.md 5.2 KB
- references/citation.bib 1.8 KB
- references/cross-database-linking.md 3.9 KB
- references/fetch-and-resolve.md 5.5 KB
- references/search-and-discovery.md 4.8 KB
- references/utilities.md 1.3 KB
- scripts/pubmed_api.py 21 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 6d ago First seen · 186 lines · 79 tokens per session scan A f1f4a89fb2b7
pubmed-database is a skill published in the GitHub repository google-deepmind/science-skills (2,835 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 79 tokens to every session and 2,007 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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