pubmed-mcp-server

v2.9.4

Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.

public 10 tools 1 resources 1 prompts protocol 2025-11-25 github cyanheads/pubmed-mcp-server

pubmed.caseyjhand.com/mcp

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

codex mcp add pubmed-mcp-server --url https://pubmed.caseyjhand.com/mcp

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

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

{
  "mcpServers": {
    "pubmed-mcp-server": {
      "command": "bunx",
      "args": [
        "mcp-remote",
        "https://pubmed.caseyjhand.com/mcp"
      ],
      "env": {
        "NCBI_API_KEY": "your-ncbi-api-key",
        "NCBI_ADMIN_EMAIL": "you@example.com",
        "UNPAYWALL_EMAIL": "you@example.com"
      }
    }
  }
}

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

curl -X POST https://pubmed.caseyjhand.com/mcp \
  -H "Content-Type: application/json" \
  -H "MCP-Protocol-Version: 2025-11-25" \
  -d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-11-25","capabilities":{},"clientInfo":{"name":"curl","version":"1.0.0"}}}'

Built on@cyanheads/mcp-ts-core v0.10.6

Tools

pubmed_search_articles

open-world

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.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_search_articles",
    "arguments": {
      "query": "<query>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "minLength": 1,
      "description": "PubMed search query (supports full NCBI syntax)"
    },
    "maxResults": {
      "default": 20,
      "description": "Maximum results to return",
      "type": "integer",
      "minimum": 1,
      "maximum": 1000
    },
    "offset": {
      "default": 0,
      "description": "Result offset for pagination (0-based)",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    },
    "sort": {
      "default": "relevance",
      "description": "Sort order: relevance (default), pub_date (newest first), author, or journal",
      "type": "string",
      "enum": [
        "relevance",
        "pub_date",
        "author",
        "journal"
      ]
    },
    "dateRange": {
      "description": "Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range.",
      "type": "object",
      "properties": {
        "minDate": {
          "type": "string",
          "pattern": "^$|^\\d{4}([/\\-.]\\d{1,2}([/\\-.]\\d{1,2})?)?$",
          "description": "Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound"
        },
        "maxDate": {
          "type": "string",
          "pattern": "^$|^\\d{4}([/\\-.]\\d{1,2}([/\\-.]\\d{1,2})?)?$",
          "description": "End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound"
        },
        "dateType": {
          "default": "pdat",
          "description": "Date type: pdat (publication), mdat (modification), edat (entrez)",
          "type": "string",
          "enum": [
            "pdat",
            "mdat",
            "edat"
          ]
        }
      },
      "required": [
        "minDate",
        "maxDate",
        "dateType"
      ],
      "additionalProperties": false
    },
    "publicationTypes": {
      "description": "Filter by publication type (e.g. \"Review\", \"Clinical Trial\", \"Meta-Analysis\"). Multiple values are OR'd — any match qualifies.",
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "author": {
      "description": "Filter by author name (e.g. \"Smith J\")",
      "type": "string"
    },
    "journal": {
      "description": "Filter by journal name",
      "type": "string"
    },
    "meshTerms": {
      "description": "Filter by MeSH terms. Multiple terms are AND'd — all must match.",
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "language": {
      "description": "Filter by language (e.g. \"english\")",
      "type": "string"
    },
    "hasAbstract": {
      "description": "Only include articles with abstracts",
      "type": "boolean"
    },
    "freeFullText": {
      "description": "Only include free full text articles",
      "type": "boolean"
    },
    "species": {
      "description": "Filter by species",
      "type": "string",
      "enum": [
        "humans",
        "animals"
      ]
    },
    "summaryCount": {
      "default": 0,
      "description": "Fetch brief summaries for top N results (0 = PMIDs only)",
      "type": "integer",
      "minimum": 0,
      "maximum": 50
    }
  },
  "required": [
    "query",
    "maxResults",
    "offset",
    "sort",
    "summaryCount"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_fetch_articles

open-world

Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_fetch_articles",
    "arguments": {
      "pmids": "<pmids>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "pmids": {
      "minItems": 1,
      "maxItems": 200,
      "type": "array",
      "items": {
        "type": "string",
        "pattern": "^\\d+$"
      },
      "description": "PubMed IDs to fetch"
    },
    "includeMesh": {
      "default": true,
      "description": "Include MeSH terms",
      "type": "boolean"
    },
    "includeGrants": {
      "default": false,
      "description": "Include grant information",
      "type": "boolean"
    }
  },
  "required": [
    "pmids",
    "includeMesh",
    "includeGrants"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_fetch_fulltext

open-world

Fetch full-text articles from PubMed Central with structured sections 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. Provide exactly one of `pmcids` (PMC IDs directly), `pmids` (PubMed IDs, auto-resolved), or `dois` (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers).

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_fetch_fulltext",
    "arguments": {}
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "pmcids": {
      "description": "PMC IDs to fetch (e.g. [\"PMC9575052\"]). Provide exactly one of `pmcids`, `pmids`, or `dois`.",
      "minItems": 1,
      "maxItems": 10,
      "type": "array",
      "items": {
        "type": "string",
        "pattern": "^(?:PMC)?\\d+$"
      }
    },
    "pmids": {
      "description": "PubMed IDs. Provide exactly one of `pmcids`, `pmids`, or `dois`. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available.",
      "minItems": 1,
      "maxItems": 10,
      "type": "array",
      "items": {
        "type": "string",
        "pattern": "^\\d+$"
      }
    },
    "dois": {
      "description": "DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled.",
      "minItems": 1,
      "maxItems": 10,
      "type": "array",
      "items": {
        "type": "string",
        "minLength": 3
      }
    },
    "includeReferences": {
      "default": false,
      "description": "Include reference list. Applies to `source=pmc` results only.",
      "type": "boolean"
    },
    "maxSections": {
      "description": "Maximum top-level body sections. Applies to `source=pmc` results only.",
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    },
    "sections": {
      "description": "Filter to specific sections by title, case-insensitive (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). Applies to `source=pmc` results only.",
      "type": "array",
      "items": {
        "type": "string"
      }
    }
  },
  "required": [
    "includeReferences"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_format_citations

open-world

Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris, vancouver). Pass a single style as a string or multiple as an array.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_format_citations",
    "arguments": {
      "pmids": "<pmids>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "pmids": {
      "minItems": 1,
      "maxItems": 50,
      "type": "array",
      "items": {
        "type": "string",
        "pattern": "^\\d+$"
      },
      "description": "PubMed IDs to cite"
    },
    "format": {
      "default": "apa",
      "description": "Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver.",
      "anyOf": [
        {
          "type": "string",
          "enum": [
            "apa",
            "mla",
            "bibtex",
            "ris",
            "vancouver"
          ],
          "description": "Single citation style. One of: apa, mla, bibtex, ris, vancouver."
        },
        {
          "minItems": 1,
          "type": "array",
          "items": {
            "type": "string",
            "enum": [
              "apa",
              "mla",
              "bibtex",
              "ris",
              "vancouver"
            ]
          },
          "description": "Multiple citation styles to generate. Each entry: apa, mla, bibtex, ris, or vancouver."
        }
      ]
    }
  },
  "required": [
    "pmids",
    "format"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_find_related

open-world

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.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_find_related",
    "arguments": {
      "pmid": "<pmid>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "pmid": {
      "type": "string",
      "pattern": "^\\d+$",
      "description": "Source PubMed ID"
    },
    "relationship": {
      "default": "similar",
      "description": "Relationship type: similar (content-based), cited_by (articles citing this one), references (articles this one cites)",
      "type": "string",
      "enum": [
        "similar",
        "cited_by",
        "references"
      ]
    },
    "maxResults": {
      "default": 10,
      "description": "Maximum related articles",
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    },
    "offset": {
      "default": 0,
      "description": "Result offset for pagination (0-based); page through results by incrementing by maxResults",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "required": [
    "pmid",
    "relationship",
    "maxResults",
    "offset"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_spell_check

open-world

Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_spell_check",
    "arguments": {
      "query": "<query>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "minLength": 2,
      "description": "PubMed search query to spell-check"
    }
  },
  "required": [
    "query"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_lookup_mesh

open-world

Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_lookup_mesh",
    "arguments": {
      "query": "<query>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "minLength": 1,
      "description": "MeSH descriptor name or free-text term to look up"
    },
    "maxResults": {
      "default": 10,
      "description": "Maximum results",
      "type": "integer",
      "minimum": 1,
      "maximum": 50
    },
    "includeDetails": {
      "default": true,
      "description": "Fetch full MeSH records (scope notes, tree numbers, entry terms)",
      "type": "boolean"
    }
  },
  "required": [
    "query",
    "maxResults",
    "includeDetails"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_lookup_citation

open-world

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 year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_lookup_citation",
    "arguments": {
      "citations": "<citations>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "citations": {
      "minItems": 1,
      "maxItems": 25,
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "journal": {
            "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\")",
            "type": "string"
          },
          "year": {
            "description": "Publication year (e.g., \"1991\")",
            "type": "string"
          },
          "volume": {
            "description": "Volume number",
            "type": "string"
          },
          "firstPage": {
            "description": "First page number",
            "type": "string"
          },
          "authorName": {
            "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\")",
            "type": "string"
          },
          "key": {
            "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted.",
            "type": "string"
          }
        },
        "additionalProperties": false,
        "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match."
      },
      "description": "Citations to look up. More fields = better match accuracy."
    }
  },
  "required": [
    "citations"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_convert_ids

open-world

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.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_convert_ids",
    "arguments": {
      "ids": "<ids>",
      "idType": "<idType>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "ids": {
      "minItems": 1,
      "maxItems": 50,
      "type": "array",
      "items": {
        "type": "string",
        "minLength": 1
      },
      "description": "Article identifiers to convert. All IDs must be the same type. DOIs: \"10.1093/nar/gks1195\", PMIDs: \"23193287\", PMCIDs: \"PMC3531190\"."
    },
    "idType": {
      "type": "string",
      "enum": [
        "pmcid",
        "pmid",
        "doi"
      ],
      "description": "The type of IDs being submitted. Required so the API can unambiguously resolve them."
    }
  },
  "required": [
    "ids",
    "idType"
  ],
  "additionalProperties": false
}

view source ↗

pubmed_europepmc_search

open-world

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`.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pubmed_europepmc_search",
    "arguments": {
      "query": "<query>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "minLength": 1,
      "description": "Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:\"<pmid>\" AND SRC:MED`. Free text is matched broadly across abstract/title/keywords."
    },
    "pageSize": {
      "default": 25,
      "description": "Results per page. Max 100 per EPMC API.",
      "type": "integer",
      "minimum": 1,
      "maximum": 100
    },
    "cursorMark": {
      "default": "*",
      "description": "Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` for subsequent pages.",
      "type": "string"
    },
    "sources": {
      "description": "Filter to specific EPMC sources. Defaults to MED, PMC, PPR when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: MED, PMC, PPR, PAT, AGR.",
      "minItems": 1,
      "type": "array",
      "items": {
        "type": "string",
        "enum": [
          "MED",
          "PMC",
          "PPR",
          "PAT",
          "AGR"
        ]
      }
    },
    "resultType": {
      "default": "core",
      "description": "`core` returns abstract, IDs, dates, license; `lite` is a smaller payload with IDs and titles only.",
      "type": "string",
      "enum": [
        "core",
        "lite"
      ]
    },
    "sort": {
      "description": "Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date.",
      "type": "string"
    }
  },
  "required": [
    "query",
    "pageSize",
    "cursorMark",
    "resultType"
  ],
  "additionalProperties": false
}

view source ↗

Resources

database-info

PubMed database metadata including field list, last update date, and record count.

uri pubmed://database/info mime application/json

Prompts

research_plan

Generate a structured research plan outline for a biomedical research project.

titlerequired — Project title
goalrequired — Primary research goal
keywordsrequired — Research keywords (comma-separated)
organism — Target organism
includeAgentPrompts — Include inline guidance blocks under each phase with execution-time hints ("true" or "false")