@cyanheads/biorxiv-mcp-server

v0.1.6 pre-1.0

Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. STDIO or Streamable HTTP.

public 5 tools protocol 2025-11-25 github cyanheads/biorxiv-mcp-server

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

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

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

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

{
  "mcpServers": {
    "biorxiv-mcp-server": {
      "command": "bunx",
      "args": [
        "@cyanheads/biorxiv-mcp-server@latest"
      ]
    }
  }
}

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

curl -X POST https://biorxiv.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 v0.9.6

Tools

biorxiv_list_categories

List valid subject category strings for bioRxiv and medRxiv. Use these strings as the `category` filter in biorxiv_list_recent to narrow results to a specific field. The taxonomy is static and maintained in-server; run this tool before filtering to get the current valid values.

read

invocation

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

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {},
  "additionalProperties": false
}

view source ↗

biorxiv_list_recent

open-world

List preprints posted or revised within a date interval, optionally scoped to one server or a subject category. Returns 30 preprints per page (fixed by the API); pass `cursor` as an integer offset (0, 30, 60, …) to step through additional pages. When server="both" (default), per-server pagination state is returned separately — use each server's `cursor` field for independent advancement. Category filtering is applied server-side; call biorxiv_list_categories for valid category strings.

read

invocation

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "biorxiv_list_recent",
    "arguments": {
      "start_date": "<start_date>",
      "end_date": "<end_date>"
    }
  }
}

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "start_date": {
      "type": "string",
      "description": "Start of the date interval (YYYY-MM-DD)."
    },
    "end_date": {
      "type": "string",
      "description": "End of the date interval (YYYY-MM-DD)."
    },
    "server": {
      "default": "both",
      "description": "Server to query. \"both\" fans out to bioRxiv and medRxiv in parallel.",
      "type": "string",
      "enum": [
        "biorxiv",
        "medrxiv",
        "both"
      ]
    },
    "category": {
      "description": "Subject category filter applied server-side. Use biorxiv_list_categories for valid values.",
      "type": "string"
    },
    "cursor": {
      "default": 0,
      "description": "Integer page offset (0, 30, 60, …). Defaults to 0 (first page).",
      "type": "integer",
      "minimum": 0,
      "maximum": 9007199254740991
    }
  },
  "required": [
    "start_date",
    "end_date",
    "server",
    "cursor"
  ],
  "additionalProperties": false
}

view source ↗

biorxiv_get_preprint

open-world

Fetch full metadata, abstract, all revision history, full-text/PDF links, and published-journal DOI for one or more preprints by DOI. Each DOI returns all revisions in one response. When server="both" (default), each DOI is checked against both bioRxiv and medRxiv; the response includes which server the preprint was found on. Per-DOI failures are surfaced in failed[] rather than aborting the batch. DOIs must match the pattern 10.NNNN/…

read

invocation

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

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "dois": {
      "minItems": 1,
      "maxItems": 10,
      "type": "array",
      "items": {
        "type": "string",
        "description": "Preprint DOI (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463)."
      },
      "description": "One or more preprint DOIs to look up (max 10)."
    },
    "server": {
      "default": "both",
      "description": "Server to query. \"both\" checks bioRxiv and medRxiv in parallel for each DOI.",
      "type": "string",
      "enum": [
        "biorxiv",
        "medrxiv",
        "both"
      ]
    }
  },
  "required": [
    "dois",
    "server"
  ],
  "additionalProperties": false
}

view source ↗

biorxiv_get_published_version

open-world

Resolve a preprint DOI to its full journal publication record — journal DOI, journal name, published date, and corresponding author details. Use when the preprint's `published` field from biorxiv_get_preprint is non-null and you need the full crosswalk metadata. Returns a not-found error when the preprint is not yet published. Check biorxiv_get_preprint first to confirm the published field is populated.

read

invocation

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

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "doi": {
      "type": "string",
      "description": "Preprint DOI to resolve (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463)."
    },
    "server": {
      "default": "biorxiv",
      "description": "Server the preprint was posted on. Defaults to biorxiv.",
      "type": "string",
      "enum": [
        "biorxiv",
        "medrxiv"
      ]
    }
  },
  "required": [
    "doi",
    "server"
  ],
  "additionalProperties": false
}

view source ↗

biorxiv_search_preprints

open-world

Search preprints by keyword using EuropePMC for relevance ranking, then enrich matching DOIs with full bioRxiv/medRxiv metadata. Covers both servers by default. EuropePMC indexes new preprints within 1–2 days of posting; for preprints posted within the last day, prefer biorxiv_list_recent. The search backend is EuropePMC — bioRxiv's native search endpoint is not used.

read

invocation

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

schema

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "type": "object",
  "properties": {
    "query": {
      "type": "string",
      "minLength": 1,
      "description": "Keyword search query."
    },
    "server": {
      "default": "both",
      "description": "Server scope for enrichment. \"both\" checks all matching DOIs on both servers.",
      "type": "string",
      "enum": [
        "biorxiv",
        "medrxiv",
        "both"
      ]
    },
    "date_from": {
      "description": "Earliest first-publication date filter (YYYY-MM-DD).",
      "type": "string"
    },
    "date_to": {
      "description": "Latest first-publication date filter (YYYY-MM-DD).",
      "type": "string"
    },
    "limit": {
      "default": 25,
      "description": "Maximum results to return (1–100). Defaults to 25.",
      "type": "integer",
      "minimum": 1,
      "maximum": 100
    }
  },
  "required": [
    "query",
    "server",
    "limit"
  ],
  "additionalProperties": false
}

view source ↗