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8 clients · secrets stay placeholders

JSON (mcpServers)Claude CodeCodexOpenCodeCursorVS CodeGemini CLIGoose

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "type": "http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

claude mcp add --transport http pubmed-mcp-server https://pubmed.caseyjhand.com/mcp

[mcp_servers.pubmed-mcp-server]
url = "https://pubmed.caseyjhand.com/mcp"

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pubmed-mcp-server": {
      "type": "remote",
      "url": "https://pubmed.caseyjhand.com/mcp",
      "enabled": true
    }
  }
}

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "type": "http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=pubmed-mcp-server&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vcHVibWVkLmNhc2V5amhhbmQuY29tL21jcCJ9"
}

{
  "servers": {
    "pubmed-mcp-server": {
      "type": "http",
      "url": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "httpUrl": "https://pubmed.caseyjhand.com/mcp"
    }
  }
}

extensions:
  "pubmed-mcp-server":
    enabled: true
    name: "pubmed-mcp-server"
    type: streamable_http
    uri: "https://pubmed.caseyjhand.com/mcp"
    timeout: 300

Quality 84 / 100good

protocol88 · weight 25

pass
protocol.modernsupports 2026-07-28 (server/discover)
pass
protocol.statelessanswers without a session
pass
protocol.transportstreamable HTTP
warn
protocol.list_ttltools/list declares ttlMs 0, so clients re-fetch it on every use

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygiene79 · weight 30

pass
tools.descriptionsevery tool has a description
warn
tools.description_length1 tools have descriptions over 1,024 characters, which crowds the context
pass
tools.schemasevery tool has an object input schema
pass
tools.annotations11 of 11 tools declare readOnlyHint or destructiveHint
fail
tools.directory_hintsno tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: pubmed_convert_ids (destructiveHint, idempotentHint); pubmed_fetch_fulltext (destructiveHint, idempotentHint); pubmed_spell_check (destructiveHint, idempotentHint); …
pass
tools.token_costabout 7,583 tokens to load every tool
pass
tools.api_dumptools are not a one-to-one API dump

stability75 · weight 15

warn
stability.changes26 tool changes in 30 days
pass
stability.rug_pullno tool changed its meaning under the same name

dependencies100 · weight 15

pass
deps.known_vulnsno known advisory in 170 resolved packages
pass
deps.mcp_sdk_version@modelcontextprotocol/core 2.3.1, no known advisory
pass
deps.resolvable@cyanheads/[email protected], @cyanheads/[email protected] resolved: 170 packages

11 tools, about 7,583 tokens to load them all · tool set 7cf1f21476e1 · tools last changed 2026-10-12 · checked 2026-10-20 12:45 UTC

Tool changes

2026-10-12pubmed_europepmc_fetchchangeddescription, output schema
before
Fetch complete Europe PMC records — including the full, untruncated abstract — for records addressed by `source` plus `epmcId`. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; pass those hits' `source` and `epmcId` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call. Set `maxResponseCharacters` to bound the whole response: records past the ceiling are deferred whole and listed in `deferred.records` for a follow-up call.
after · 82% of words in common
Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as `records: [{ source, epmcId }]`, an array even for one record. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; copy each hit's `source` and `epmcId` into `records` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call. Set `maxResponseCharacters` to bound the whole response: records past the ceiling are deferred whole and listed in `deferred.records` for a follow-up call.
2026-10-12pubmed_europepmc_searchchangeddescription, input schema, output schema
before
Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit’s `source` and `epmcId` to `pubmed_europepmc_fetch` for the complete abstract.
after · 98% of words in common
Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete abstract.
2026-10-12pubmed_lookup_meshchangedoutput schema
2026-10-12pubmed_spell_checkchangeddescription, output schema
before
Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled — every misspelled token is corrected in one call (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`), and `hasSuggestion` is false when NCBI has no change to offer. Re-run the search with `corrected`.
after · 54% of words in common
Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spacing, and gene symbols stay as written (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`). Words in all capitals, with digits or non-ASCII letters, or differing only in case are never changed, words after a number or symbol ESpell skips are left as written, and `hasSuggestion` is false when no correction was applied. Re-run the search with `corrected`.
2026-10-12pubmed_fetch_fulltextchangedinput schema, output schema
2026-10-12pubmed_fetch_articleschangedoutput schema
2026-10-09pubmed_europepmc_fetchchangedinput schema
2026-10-09pubmed_format_citationschangeddescription, output schema
before
Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array.
after · 57% of words in common
Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in `notices`; Vancouver and APA also cite a retraction in the reference itself.
2026-10-09pubmed_fetch_fulltextchangeddescription, input schema, output schema
before
Fetch full-text articles from PubMed Central with structured sections, tables, and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Name articles by `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), `dois` (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers), or any mix of the three — up to 10 distinct identifiers per call; an article several of them name is fetched and returned once. Two independent character controls: `maxCharacters` caps body text per article, `maxResponseCharacters` caps the whole response and defers articles past the ceiling whole, listing them in `deferred.ids` for a follow-up call.
after · 91% of words in common
Fetch full-text articles from PubMed Central as structured sections — the body, then back matter such as acknowledgments, declarations, and appendices — with tables and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Name articles by `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), `dois` (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers), or any mix of the three — up to 50 distinct identifiers; the first 10 are fetched per call, the rest returned in `overLimit`; an article several of them name is fetched and returned once. Two independent character controls: `maxCharacters` caps body text per article, `maxResponseCharacters` caps the whole response and defers articles past the ceiling whole, listing them in `deferred.ids` for a follow-up call.
2026-10-09pubmed_fetch_articleschangeddescription, input schema, output schema
before
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices. Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.
after · 84% of words in common
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices; grants and the members of a collective author are opt-in (`includeGrants`, `includeInvestigators`). Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.

Showing the latest 10. Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 94 / 100

provenance80

liveness100

freshness100

hygiene100

+repository +namespace-matches-repo +reachable +uptime-99% +updated-8d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

@cyanheads/[email protected] npm84 dependencies, resolved · MCP SDK @modelcontextprotocol/core 2.3.1 · advisories checked 2026-10-19

No known advisory affects this dependency graph.

@cyanheads/[email protected] npm84 dependencies, resolved · MCP SDK @modelcontextprotocol/core 2.3.1 · advisories checked 2026-10-19

No known advisory affects this dependency graph.

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

remote	auth	reachable	uptime 30d	p50	protocol	last ok
`https://pubmed.caseyjhand.com/mcp` streamable-http	none	yes	99%	170 ms	2026-07-28	2026-10-20

package	registry	version	runtime	secrets
`@cyanheads/pubmed-mcp-server`	npm	2.10.22	npx
`@cyanheads/pubmed-mcp-server`	npm	2.10.22	npx

Tools (11)

`pubmed_convert_ids`read-only	Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.
`pubmed_europepmc_fetch`read-only	Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as `records: [{ source, epmcId }]`, an array even for one record. Pairs with `pubmed_europepmc_search`, which returns bounded `abstractSnippet` values and flags cut ones with `abstractTruncated: true`; copy each hit's `source` and `epmcId` into `records` here to read the whole abstract. This is the retrieval path for preprint (`PPR`), patent (`PAT`), and Agricola (`AGR`) records, which frequently carry no PMID and no DOI, so `pubmed_fetch_articles` and `pubmed_fetch_fulltext` cannot address them. Up to 25 records per call. Set `maxResponseCharacters` to bound the whole response: records past the ceiling are deferred whole and listed in `deferred.records` for a follow-up call.
`pubmed_europepmc_search`read-only	Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete abstract.
`pubmed_fetch_articles`read-only	Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices; grants and the members of a collective author are opt-in (`includeGrants`, `includeInvestigators`). Set `maxResponseCharacters` to bound the whole response: articles past the ceiling are deferred whole and listed in `deferred.ids` for a follow-up call.
`pubmed_fetch_fulltext`read-only	Fetch full-text articles from PubMed Central as structured sections — the body, then back matter such as acknowledgments, declarations, and appendices — with tables and references. When PMC misses, transparently falls back to Europe PMC `fullTextXML` (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Name articles by `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), `dois` (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers), or any mix of the three — up to 50 distinct identifiers; the first 10 are fetched per call, the rest returned in `overLimit`; an article several of them name is fetched and returned once. Two independent character controls: `maxCharacters` caps body text per article, `maxResponseCharacters` caps the whole response and defers articles past the ceiling whole, listing them in `deferred.ids` for a follow-up call.
`pubmed_find_related`read-only	Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.
`pubmed_format_citations`read-only	Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in `notices`; Vancouver and APA also cite a retraction in the reference itself.
`pubmed_lookup_citation`read-only	Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or a four-digit year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.
`pubmed_lookup_mesh`read-only	Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.
`pubmed_search_articles`read-only	Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.
`pubmed_spell_check`read-only	Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin `pubmed_search_articles` result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spacing, and gene symbols stay as written (`alzhiemer diseese treatmnt outcomse` → `alzheimer disease treatment outcomes`). Words in all capitals, with digits or non-ASCII letters, or differing only in case are never changed, words after a number or symbol ESpell skips are left as written, and `hasSuggestion` is false when no correction was applied. Re-run the search with `corrected`.

Schemas: list_tools.

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Official server.json

{
  "name": "io.github.cyanheads/pubmed-mcp-server",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://pubmed.caseyjhand.com/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "2.10.22",
  "packages": [
    {
      "version": "2.10.22",
      "transport": {
        "type": "stdio"
      },
      "identifier": "@cyanheads/pubmed-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        },
        {
          "name": "NCBI_API_KEY",
          "format": "string",
          "description": "NCBI API key for higher rate limits (10 req/s vs 3 req/s)."
        },
        {
          "name": "NCBI_ADMIN_EMAIL",
          "format": "string",
          "description": "Contact email sent with NCBI requests (recommended by NCBI)."
        },
        {
          "name": "UNPAYWALL_EMAIL",
          "format": "string",
          "description": "Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC."
        }
      ]
    },
    {
      "version": "2.10.22",
      "transport": {
        "url": "http://localhost:3010/mcp",
        "type": "streamable-http"
      },
      "identifier": "@cyanheads/pubmed-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_TRANSPORT_TYPE",
          "value": "http",
          "format": "string",
          "description": "Selects the HTTP transport."
        },
        {
          "name": "MCP_HTTP_HOST",
          "format": "string",
          "default": "127.0.0.1",
          "description": "The hostname for the HTTP server."
        },
        {
          "name": "MCP_HTTP_PORT",
          "format": "string",
          "default": "3010",
          "description": "The port to run the HTTP server on."
        },
        {
          "name": "MCP_HTTP_ENDPOINT_PATH",
          "format": "string",
          "default": "/mcp",
          "description": "The endpoint path for the MCP server."
        },
        {
          "name": "MCP_PUBLIC_URL",
          "format": "string",
          "description": "Public origin override for deployments behind a TLS-terminating reverse proxy (e.g. https://mcp.example.com)."
        },
        {
          "name": "MCP_AUTH_MODE",
          "format": "string",
          "default": "none",
          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        },
        {
          "name": "NCBI_API_KEY",
          "format": "string",
          "description": "NCBI API key for higher rate limits (10 req/s vs 3 req/s)."
        },
        {
          "name": "NCBI_ADMIN_EMAIL",
          "format": "string",
          "description": "Contact email sent with NCBI requests (recommended by NCBI)."
        },
        {
          "name": "UNPAYWALL_EMAIL",
          "format": "string",
          "description": "Contact email for Unpaywall. When set, pubmed_fetch_fulltext falls back to Unpaywall open-access copies for DOIs not in PMC."
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/cyanheads/pubmed-mcp-server",
    "source": "github"
  },
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms."
}