pubmed-proxy-mcp

MCP server and CLI for NCBI PubMed E-utilities with built-in rate limiting.

Features

• PubMed search — Full query syntax with field tags, boolean operators, date ranges, pagination, and sorting

• Article metadata — Fetch title, authors, journal, year, DOI, and abstract for any PMID

• Batch lookup — Fetch metadata for up to 20 PMIDs at once

• Full-text retrieval — Get full article text from PubMed Central (when available)

• BibTeX citations — Generate BibTeX entries from PMID or DOI (with CrossRef fallback)

• Bibliography management — Add citations to .bib files, search, list, validate, and batch-initialize

• BibTeX correction — Correct .bib files against authoritative NCBI/CrossRef metadata with smart field comparison

• Rate limiting — Built-in token bucket (10 req/s NCBI, 1 req/s CrossRef)

Related MCP server: mcp-pubmed

Quick Start for LLM Agents

If you are an LLM agent that has been pointed to this tool for literature research, follow these steps:

1. Check that the NCBI API key is configured (recommended but optional):

echo $NCBI_API_KEY

If empty, commands will still work but at a lower rate limit (3 req/s instead of 10 req/s). To get the faster rate, set an API key:

export NCBI_API_KEY="your-api-key"

Or pass it per-command with --api-key <key>. To obtain a key: create an account at https://www.ncbi.nlm.nih.gov/account/, then go to Settings > API Key Management > Create an API Key.

2. If using MCP tools (e.g. via Claude Desktop), the MCP server must be configured in the client. The CLI commands below work standalone without the MCP server.

3. Typical research workflow:

# Search for relevant articles
pubmed-proxy search "your topic here" --summaries --max 10

# Get full metadata + abstract for interesting PMIDs
pubmed-proxy lookup 23381990

# Get full-text if available (PMC only)
pubmed-proxy lookup --full-text 23381990

# Generate BibTeX citations for references
pubmed-proxy citation 23381990 16855256 >> references.bib

Installation

pip install -e .            # Core (MCP server + basic CLI)
pip install -e ".[bib]"     # With bibliography management (bibtexparser)

Requires Python 3.10+. An NCBI API key is recommended for higher rate limits (see Quick Start above).

MCP Server

Run as an MCP server (stdio transport). Works without an API key (3 req/s) or with one (10 req/s):

python -m pubmed_proxy_mcp

MCP Tools

CLI Reference

An NCBI API key is optional but recommended. Without one, the rate limit is 3 req/s instead of 10 req/s. If not set, a warning is printed to stderr but commands still work.

echo $NCBI_API_KEY    # If empty, commands work at 3 req/s

To use a key, either export NCBI_API_KEY=<key> or pass --api-key <key> to any command.

pubmed-proxy server — Shared Rate-Limiting Proxy

Note: The proxy server is only needed when running multiple CLI commands in parallel (e.g. from multiple subagents). For single-command usage, the CLI works fine on its own with its built-in rate limiter — no server required.

When running parallel commands, each process has its own rate limiter. To share a single rate limiter across all processes, start the proxy server first:

# Terminal 1: start the shared proxy server
pubmed-proxy server                    # default port 8765
pubmed-proxy server --port 9000        # custom port

Then point CLI commands at it with --server:

# Terminal 2+: commands share the proxy's rate limiter
pubmed-proxy --server http://localhost:8765 search "CRISPR" --max 10
pubmed-proxy --server http://localhost:8765 lookup 23381990

The MCP server also auto-detects the proxy: if pubmed-proxy server is running on port 8765 when the MCP server starts, it will use the shared rate limiter automatically. Set PUBMED_PROXY_URL to override the proxy URL for the MCP server.

Arguments:

Global --server flag:

pubmed-proxy search — Search PubMed

Search PubMed using full NCBI query syntax. Supports field-specific tags, boolean operators (AND, OR, NOT), and MeSH terms.

Arguments:

Query syntax examples:

• "E. coli iron regulation" — keyword search

• "Smith[Author] AND cancer[Title]" — field-specific search

• "CRISPR[Title] AND 2024[PDAT]" — with publication date tag

• "breast cancer AND review[PT]" — filter by publication type

• "Nature[Journal] AND gene editing" — journal-specific search

Output without --summaries:

Found 1543 results (showing 1-20):

  38471234
  38469012
  ...

Output with --summaries:

Found 1543 results (showing 1-5):

  PMID: 38471234
  Title: CRISPR-Cas9 gene editing in E. coli
  Authors: Smith, JD; Doe, A; Lee, B (+4 more)
  Journal: Nature Biotechnology (2024)

  PMID: 38469012
  Title: Another relevant paper
  Authors: Jones, C; Wang, X
  Journal: Science (2024)

Examples:

# Basic keyword search
pubmed-proxy search "antibiotic resistance"

# Field-specific with boolean operators
pubmed-proxy search "Smith[Author] AND cancer[Title]"

# Filter by date range (publication date)
pubmed-proxy search "CRISPR" --min-date 2023/01/01 --max-date 2024/12/31 --date-type pdat

# Sort by publication date, get 10 results
pubmed-proxy search "biofilm" --max 10 --sort pub_date

# Page 2 of results (results 11-20)
pubmed-proxy search "biofilm" --max 10 --page 1

# Include metadata summaries for quick scanning
pubmed-proxy search "antibiotic resistance" --summaries --max 5

pubmed-proxy lookup — Get Article Metadata

Fetch metadata and abstract for one or more PubMed articles by PMID.

Arguments:

Output (metadata mode):

PMID: 23381990
Valid: Yes
Title: The Fur regulon of pathogenic Neisseria
Authors: Smith, JD, Doe, A, Lee, B, Wang, X, Jones, C
Journal: Journal of Bacteriology (2013)
DOI: 10.1128/JB.01411-12
Abstract: The ferric uptake regulator (Fur) is a transcription factor...

For multiple PMIDs, each article's metadata is separated by a blank line. Invalid PMIDs return Valid: No with an error message.

Output (full-text mode):

PMID: 23381990 (Full Text)
PMCID: PMC3697534

## Introduction

The ferric uptake regulator (Fur) is a global...

## Results

We identified 47 genes...

If the article is not available in PMC, shows: Error: Full text not available in PMC

Examples:

# Single article metadata + abstract
pubmed-proxy lookup 23381990

# Batch lookup (up to 20 PMIDs)
pubmed-proxy lookup 23381990 16855256 25157846

# Full article text (PMC only, first PMID only)
pubmed-proxy lookup --full-text 23381990

pubmed-proxy citation — Fetch BibTeX Citations

Generate BibTeX @article entries for PubMed articles. Output goes to stdout and can be piped or appended to .bib files. Citekeys use the format pmid_XXXXXXXX.

Arguments:

*Provide either pmids or --doi.

Output:

@article{pmid_23381990,
  author = {Smith, JD and Doe, A},
  title = {{The Fur regulon of pathogenic Neisseria}},
  journal = {J Bacteriol},
  year = {2013},
  volume = {195},
  number = {14},
  pages = {3159-3170},
  doi = {10.1128/JB.01411-12},
  pmid = {23381990}
}

Multiple PMIDs produce multiple entries separated by blank lines. DOI-only entries (not in PubMed) use citekey format doi_<sanitized_doi>.

Examples:

# Single PMID to stdout
pubmed-proxy citation 23381990

# Multiple PMIDs, append to a file
pubmed-proxy citation 23381990 16855256 25157846 >> references.bib

# By DOI (tries NCBI first, falls back to CrossRef)
pubmed-proxy citation --doi 10.1128/JB.01411-12

pubmed-proxy doi2pmid — Convert DOI to PMID

Look up the PubMed ID for a given DOI.

Arguments:

Output:

DOI: 10.1038/s41467-019-13483-w
PMID: 31784527

If no PMID is found: PMID: not found

Example:

pubmed-proxy doi2pmid 10.1038/s41467-019-13483-w

pubmed-proxy correct — Correct BibTeX Files

Correct a .bib file by verifying each entry against authoritative NCBI/CrossRef metadata. For each entry, fetches correct metadata by DOI, existing PMID, or title search (with author-overlap validation to avoid wrong matches).

Requires pip install -e ".[bib]".

Smart comparison rules:

• Authors: never replaces full names with initials; expands "and others"; flags mismatches for review

• Pages: normalizes abbreviated ranges (e.g. 735-47 to 735-747); preserves LaTeX en-dashes

• Journal: prefers longer (more complete) journal name

• Title: never touched (may contain LaTeX formatting)

• Year/volume/number/DOI: trusts authoritative source

Arguments:

Output:

  entry1_key: OK via DOI
  entry2_key: FIXED 2 field(s) via DOI
    year: 2012 -> 2013
    pages: 735-47 -> 735-747
  entry3_key: FAIL could not fetch (no DOI/PMID)

Summary: 15 entries processed
  Verified OK:  12
  Corrected:    2
  Failed:       1
  Skipped:      0
Output: corrected.bib

Examples:

# Correct to a new output file
pubmed-proxy correct -i references.bib -o corrected.bib

# Correct in-place (creates references.bib.bak backup)
pubmed-proxy correct -i references.bib

pubmed-proxy bib — Bibliography Management

Manage .bib files: add citations, search, list, validate, and batch-initialize. All bib subcommands accept --dir DIR to specify the directory containing .bib files (default: current directory).

Requires pip install -e ".[bib]" (bibtexparser).

bib fetch — Add Citation to .bib File

Fetch a BibTeX citation by PMID or DOI and add it to a .bib file. Automatically deduplicates — skips entries whose citekey already exists.

*Provide either identifiers or --doi.

pubmed-proxy bib fetch 23381990 --bib Fur.bib
pubmed-proxy bib fetch 23381990 16855256 --bib refs.bib
pubmed-proxy bib fetch --doi 10.1128/JB.01411-12 --bib Fur.bib
pubmed-proxy bib fetch 23381990 --bib refs.bib --dir ./citations

Output: Added: pmid_23381990 or Already exists: pmid_23381990

bib search — Search Across .bib Files

Search all .bib files in a directory for a keyword. Searches citekeys and all fields (title, author, journal, etc.). Case-insensitive.

pubmed-proxy bib search "Fur"
pubmed-proxy bib search "iron regulation" --dir ./citations

Output:

Found 3 entries matching 'Fur':

  [Fur.bib] @pmid_23381990: The Fur regulon of pathogenic Neisseria
  [Fur.bib] @pmid_16855256: Fur-mediated iron transport in E. coli
  [iron.bib] @pmid_25157846: Iron homeostasis and Fur regulation

bib list — List Entries in .bib Files

List all entries in all .bib files, or in a specific file.

pubmed-proxy bib list --dir ./citations
pubmed-proxy bib list --bib Fur.bib --dir ./citations

Output:

Fur.bib (3 entries):
  @pmid_23381990: The Fur regulon of pathogenic Neisseria (2013)
  @pmid_16855256: Fur-mediated iron transport in E. coli (2006)
  @pmid_25157846: Iron homeostasis and Fur regulation (2014)

bib show — Show Full BibTeX for a Citekey

Look up a citekey across all .bib files and print the complete BibTeX entry.

pubmed-proxy bib show pmid_23381990
pubmed-proxy bib show pmid_23381990 --dir ./citations

Output: the full @article{...} BibTeX block, preceded by # From <filename>.

bib validate — Validate Citekeys in Markdown

Check that all @citekey references and PMID:XXXXX patterns in a markdown file exist in the specified .bib file.

pubmed-proxy bib validate evidence.md --bib evidence.bib --dir ./citations

Output on success: OK: 5 citekeys validated, 2 raw PMIDs all in bib

Output on failure (exits with code 1):

MISSING citekeys (not in evidence.bib):
  @pmid_99999999
UNCONVERTED PMIDs (still using PMID:XXXXX format):
  PMID:12345678

bib validate-all — Validate All Evidence Files

Scan all markdown files in a directory and validate each one against its corresponding .bib file (e.g. Fur.md against Fur.bib).

pubmed-proxy bib validate-all --scan-dir ./evidence --dir ./citations

Output on success: All evidence files validated (12 bib files)

Output on failure (exits with code 1):

Fur.md: 2 missing citekey(s) — pmid_99999999, pmid_88888888
iron.md: 1 unconverted PMID(s)

Total: 3 issues across 2 files

bib init — Batch-Create .bib Files from Markdown

Scan markdown files for PMID:XXXXX references, fetch BibTeX from PubMed for each, and create per-file .bib files (e.g. Fur.md produces Fur.bib).

pubmed-proxy bib init --scan-dir ./evidence --dir ./citations

Output:

Found 47 unique PMIDs across 12 files
  Fetching PMID: 23381990...
  Fetching PMID: 16855256...
  ...
Fetched 45/47 PMIDs
Created/updated 12 .bib files in ./citations

bib stats — Citation Database Statistics

Print summary statistics for all .bib files in a directory.

pubmed-proxy bib stats --dir ./citations

Output:

Citation Database Statistics:
  .bib files:       12
  Total entries:    47
  Unique citekeys:  45

Claude Desktop Configuration

Add to your Claude Desktop config (claude_desktop_config.json):

{
  "mcpServers": {
    "pubmed": {
      "command": "python",
      "args": ["-m", "pubmed_proxy_mcp"],
      "env": {
        "NCBI_API_KEY": "your-api-key"
      }
    }
  }
}

The NCBI_API_KEY in the env block is optional but recommended for the higher 10 req/s rate limit. Without it the server works at 3 req/s. Replace "your-api-key" with your actual key from https://www.ncbi.nlm.nih.gov/account/settings/.