Pubmed Python Packages

biomcp-python

BioMCP: Biomedical Model Context Protocol

citevahti

Run unit tests on your manuscript. Check every manuscript claim against its cited evidence. Human-first, AI-second, Zotero-audited, local-first.

local-deep-research

~95% on SimpleQA (e.g. Qwen3.6-27B on a 3090). Supports all local and cloud LLMs (llama.cpp, Ollama, Google, ...). 10+ search engines - arXiv, PubMed, your private documents. Everything Local & Encrypted.

data-aggregator-mcp

Unified research-data acquisition MCP — search & fetch datasets across Zenodo, DataCite, NCBI omics (GEO/SRA/BioProject), and literature (PubMed/OpenAIRE) behind one normalized model.

paperscraper

A bibliometrics tool for publication metadata (pubmed, arxiv, medrxiv, biorxiv, chemrxiv) and citation analyses

pubmed-search-mcp

🔬 Professional MCP server for biomedical literature research — 40 tools, multi-source search (PubMed, Europe PMC, CORE, OpenAlex), full-text access, citation networks, PICO analysis, and more

biomcp-cli

BioMCP: Biomedical Model Context Protocol

pubmed-downloader

Automate downloading and processing PubMed in bulk

findpapers

Findpapers: A tool for helping researchers who are looking for related works

pmcgrab

A PMC ID in. Clean, loss-aware article JSON out. Parse PubMed Central and JATS XML for biomedical AI, RAG, search, and literature pipelines.

easy-entrez

Python REST API for Entrez E-Utilities: stateless, easy to use, reliable.

nalaf

NLP framework in python for entity recognition and relationship extraction

modulector-sdk

An open platform which provides information about miRNAs and genes from different popular databases

pmidcite

Turbocharge a PubMed literature search using citation data from the NIH

onecite

📚 Only Cite what you can verify

richcontext-scholapi

Rich Context API integrations for federating metadata discovery and exchange across multiple scholarly infrastructure providers

bibtools-pkg

Fetch papers and metadata.

pypubmed

Toolkits for NCBI Pubmed

pubmatrixpython

Python port of PubMatrixR — systematic literature co-occurrence analysis via NCBI PubMed

pubwords

All non-duplicated words as scraped from every publicly available PubMed abstract.

pubrunner

A framework to rerun text mining tools on the latest publications

pybibget

Command line utility to automatically retrieve BibTeX citations from MathSciNet, arXiv, PubMed and doi.org

bioinformatics-mcp-server

MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and sequences via NCBI & UniProt (free, no API key)

zotero-keeper

AI-powered research toolkit integrating PubMed search, Zotero management, and VS Code extension with OpenURL institutional access