Skip to main content
Glama
Sign In
BioCite-MCP

BioCite-MCP

by muslus
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

BioCite-MCP 🧬

PyPI version Python 3.10+ License: MIT MCP

BioCite-MCP is an advanced Model Context Protocol (MCP) server that acts as a real-time bridge between LLMs and academic literature databases (Europe PMC & Crossref). It eliminates citation hallucinations by forcing AI models to retrieve verified, peer-reviewed paper metadata and real DOIs directly within their workflow.

🌟 Key Features

🔍 Literature Discovery

  • search_literature: Query Europe PMC for real biological papers. Returns structured metadata including DOIs and abstracts.

  • find_related_papers: Discovers semantically related research using Europe PMC's Recommendations engine with an automated Citations/References fallback.

📝 Citation & Formatting

  • resolve_citation: Converts any DOI into publication-ready citation strings (APA or Nature style).

  • export_bibtex: Retrieves professional BibTeX entries directly via Crossref content negotiation.

🛡️ Manuscript Auditing & Support

  • audit_manuscript: Scans your text for DOIs to verify them and flags potential citations that lack DOIs.

  • summarize_paper: Fetches abstracts and prepares high-quality summarization prompts optimized for LLMs like Claude.

  • check_duplicate_citations: Uses fuzzy matching (rapidfuzz) to identify and group duplicate research in your lists.

📚 Integration

  • push_to_zotero: Seamlessly add verified papers to your Zotero library via the Web API.

Related MCP server: PubMed Advanced MCP Server

🚀 Installation

pip install biocite-mcp

Note: For development, use pip install -e . in the repository root.

🔧 Configuration

Add biocite-mcp to your MCP host configuration (e.g., claude_desktop_config.json):

{
  "mcpServers": {
    "biocite-mcp": {
      "command": "python",
      "args": ["-m", "biocite_mcp"]
    }
  }
}

🛠️ Usage Examples

  1. Search: "Find recent papers about DREB2A drought stress in tomato."

  2. Resolve: "Format the citation for DOI 10.1093/jxb/erx393 in Nature style."

  3. Analyze: "Audit this manuscript draft for citation accuracy: [Your Text Here]" (Pro-tip: Use Claude's Filesystem MCP to read your manuscript file and pipe the content directly into this tool!)

  4. Export: "Give me the BibTeX for 10.1111/j.1365-313X.2006.02701.x"

📜 License

This project is licensed under the MIT License - see the LICENSE file for details.

Developed by ZaEyAsa — Your Advanced Agentic Bio-Citation Assistant.

Available Tools

8 tools
audit_manuscriptA

Scan a text for DOIs and citations, validating them and identifying missing DOIs.

Args: text: The manuscript text (markdown, txt, etc.) to audit.

Inputs: text (required). Returns: result

check_duplicate_citationsA

Identify duplicate papers in a list based on DOI and Title similarity.

Args: papers_json: A JSON string containing a list of paper objects with 'title' and optional 'doi'. threshold: Similarity threshold (0-100) for title matching.

Inputs: papers_json (required), threshold. Returns: result

export_bibtexC

Retrieve the BibTeX citation for a given DOI.

Args: doi: The DOI of the paper to export.

Inputs: doi (required). Returns: result

find_related_papersA

Find semantically related papers based on a given DOI.

Args: doi: The DOI of the source paper. limit: Maximum number of related papers to return (1-10)

Inputs: doi (required), limit. Returns: result

push_to_zoteroA

Push a paper's metadata to a Zotero library.

Args: doi: The DOI of the paper to add. zotero_key: Your Zotero API Key (Secret). library_id: Your Zotero User ID or Group ID. library_type: "user" or "group". collection_id: (Optional) ID of the collection to add the paper to.

Inputs: doi (required), zotero_key (required), library_id (required), library_type, +1 more. Returns: result

resolve_citationA

Convert a known DOI into a formatted, publication-ready citation string.

Args: doi: A valid DOI string (e.g., 10.1093/jxb/erx393) style: Citation style: "apa" or "nature"

Inputs: doi (required), style. Returns: result

search_literatureB

Query Europe PMC to retrieve real, peer-reviewed papers matching a biological query.

Args: query: Free-text search query (e.g., "DREB2A drought stress tomato") limit: Maximum number of results to return (1-25)

Inputs: query (required), limit. Returns: result

summarize_paperA

Fetch a paper's abstract and metadata for the LLM to summarize.

Args: doi: The DOI of the paper to summarize.

Inputs: doi (required). Returns: result

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

Loading tool schema changelog…

    Deploy Server
    One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

    TDQS

    A3.8/5.0

    Scored across 8 tools

    Disambiguation5/5

    Each tool has a distinct and clearly defined purpose: scanning text for DOIs, checking duplicates, exporting citations, finding related papers, pushing to Zotero, resolving citations, searching literature, and summarizing papers. No overlap in functionality.

    Naming Consistency5/5

    All tool names follow a consistent verb_noun pattern with lowercase and underscores, e.g., 'audit_manuscript', 'export_bibtex', 'search_literature'. The naming is predictable and easy to understand.

    Tool Count5/5

    With 8 tools, the set is well-scoped for a citation management server. It covers essential operations without being overwhelming or too sparse.

    Completeness4/5

    The tools cover core citation workflows: searching, validation, export, metadata retrieval, integration with Zotero, and duplication detection. Minor gaps like batch export or import are absent but do not hinder primary use cases.

    Maintenance

    ActivityInactive
    ResponsivenessNo recent community issues

    Resources

    Related MCP Connectors

    Related MCP Servers

    • mcp-pubmed-server

      hhx465453939
      A
      license
      C
      quality
      D
      maintenance
      A PubMed MCP server that enables LLMs to search, retrieve details, and download full-text articles from PubMed, with support for batch queries, cross-referencing, and EndNote export.
      13
      47 npm
      6
      Apache 2.0

    • PubMed Advanced MCP Server

      SuyashEkhande
      A
      license
      B
      quality
      D
      maintenance
      This MCP server provides 16 intelligent tools for searching, retrieving, and linking biomedical literature from PubMed and PMC. It enables LLM applications to perform complex queries, batch processing, and cross-database linking.
      16
      8
      MIT

    • scholar-mcp

      pvliesdonk
      A
      license
      A
      quality
      B
      maintenance
      A FastMCP server for the scholarly citation landscape that enables LLMs to search, cross-reference, and retrieve prior art across papers, patents, books, and standards via multiple APIs.
      21
      712 PyPI
      3
      MIT

    • BioMCP

      qgeng1465
      F
      license
      B
      quality
      A
      maintenance
      BioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.
      73
      14
      -