What is pubmed-guide?

A guide to searching biomedical research databases and matching article identifiers. PubMed is a database of medical research citations; related sources include full-text papers, preprints, and citation metrics.

Use it to build MeSH or systematic searches, convert DOIs and PMIDs, find open copies, retrieve articles, locate preprints, and check NIH iCite metrics.

It helps avoid incorrect searches, broken identifier conversions, unavailable full text, and unsupported claims about citations or clinical-trial records.

pubmed-guide — Skill for Claude Code by cyanheads/pubmed-mcp-server

Install

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.

Any agent

npx skills add cyanheads/pubmed-mcp-server --skill pubmed-guide

Clone the repo

git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server

Made for: Claude Code.

Or install pubmed-mcp-server, the plugin that ships this one along with the rest of its 35 skills, 1 MCP server.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/cyanheads/pubmed-mcp-server/pubmed-guide/github.svg)](https://agentmods.dev/skills/cyanheads/pubmed-mcp-server/pubmed-guide)

Your own site

<a href="https://agentmods.dev/skills/cyanheads/pubmed-mcp-server/pubmed-guide"><img src="https://agentmods.dev/badge/skills/cyanheads/pubmed-mcp-server/pubmed-guide/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/cyanheads/pubmed-mcp-server/pubmed-guide"><img src="https://agentmods.dev/badge/skills/cyanheads/pubmed-mcp-server/pubmed-guide.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 82 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,486 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

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	$0.00082	$0.02486
Opus 5.5	$0.00033	$0.00994
Sonnet 5.5	$0.00016	$0.00497
Haiku 4.5	$0.00008	$0.00249

Measured 2d ago against content hash 8a0fd124e755, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

pubmed-guide scanned grade A with 0 findings 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 2d 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.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/pubmed-guide/SKILL.md · 80 lines

How it starts

The opening of the file, as written. The whole thing — 80 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Scope

Biomedical literature: PubMed records (MEDLINE, PubMed Central, NCBI Bookshelf), PMC full text, Europe PMC (adds preprints, patents, Agricola), and NIH iCite citation metrics. Keyless. NCBI_API_KEY raises NCBI's rate ceiling, UNPAYWALL_EMAIL adds an Unpaywall full-text tier, and a deployment that sets EUROPEPMC_ENABLED=false registers neither Europe PMC tool.

Full text only where an open copy exists: PMC, Europe PMC's open-access subset, or, with UNPAYWALL_EMAIL set, a copy Unpaywall finds. A subscription article outside all three comes back in unavailable.
iCite metrics are keyed by PMID, so a work PubMed doesn't index has none here.
Trial registrations appear only as accessions in pubmed_fetch_articles dataBanks; the registry record itself is a ClinicalTrials.gov server's job. Literature outside biomedicine belongs to an OpenAlex or Crossref server.

Identifiers

ID	Form	Comes from
PMID	digits	`pubmed_search_articles`, `pubmed_lookup_citation`, a `MED` hit of `pubmed_europepmc_search` (its `epmcId` is the PMID)
PMCID	`PMC` + digits	`pmcId` on `pubmed_fetch_articles` records and search summaries; `pubmed_convert_ids`
DOI	`10.…/…`	`doi` on `pubmed_fetch_articles` records and Europe PMC hits
Europe PMC `source` + `epmcId`	`PPR1306463`	`pubmed_europepmc_search` hits only; preprints and patents often carry no PMID or DOI
MeSH descriptor	its preferred name	`name` on `pubmed_lookup_mesh` results
ORCID	`0000-0002-5446-9969`	`orcid` on `pubmed_fetch_articles` authors, when the record carries one

Crosswalks:

PMID → DOI or PMCID: pubmed_fetch_articles, for any PubMed record.
DOI → PMID: pubmed_convert_ids answers only for articles in PMC; 10.1056/NEJMoa1911303 (not in PMC) fails there. Search 10.1056/NEJMoa1911303[doi] with pubmed_search_articles (returns 31535829), or DOI:"10.1056/NEJMoa1911303" with pubmed_europepmc_search, whose hit carries the PMID.
ORCID → an author's papers: 0000-0002-5446-9969[auid] in pubmed_search_articles returned 46 records. It matches only records whose author entry carries that ORCID, however the name is spelled.

Read the full file on GitHub · 80 lines

Changes

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.

2d ago First seen · 80 lines · 82 tokens per session scan A 8a0fd124e755

Subscribe to this mod's changes

pubmed-guide is a skill published in the GitHub repository cyanheads/pubmed-mcp-server (167 stars, last pushed 3d ago), licensed Apache-2.0. It adds 82 tokens to every session and 2,486 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-11-04.

NCBI Research Scientific ai-agents ai-tools mcp mcp-server model-context-protocol

pubmed-guide next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
pubmed-guidecyanheads/pubmed-mcp-server	Skill	167	3d ago	Apache-2.0	A	82	Claude Code
mitiq-error-mitigationxi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	48	Claude Code, Codex
quantum-ground-statexi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	103	Codex
quantum-amplitude-estimationxi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	63	Claude Code, Codex
quantum-groverxi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	62	Claude Code, Codex
quantum-hidden-shiftxi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	47	Claude Code, Codex
quantum-lcuxi-zhao/OpenQuantum	Skill	71	yesterday	MIT	A	61	Claude Code, Codex