PyPI Stats

Pubmed Python Packages

Python packages with the GitHub topic pubmed. Sorted by relevance, with stars and monthly downloads.
genomoncology
biomcp-python

BioMCP: Biomedical Model Context Protocol

39K 500 101
LearningCircuit
local-deep-research

Local Deep Research achieves ~95% on SimpleQA benchmark (tested with Qwen 3.6). Supports local and cloud LLMs (Ollama, Google, Anthropic, ...). Searches 10+ sources - arXiv, PubMed, web, and your private documents. Everything Local & Encrypted.

17K 5K 427
u9401066
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

6K 9 7
cthoyt
pubmed-downloader

Automate downloading and processing PubMed in bulk

5K 6 0
jannisborn
paperscraper

Tools to scrape publications & their metadata from pubmed, arxiv, medrxiv, biorxiv and chemrxiv.

4K 515 58
genomoncology
biomcp-cli

BioMCP: Biomedical Model Context Protocol

4K 500 101
dvklopfenstein
pmidcite

Get citation counts for a PubMed paper from the command line

2K 34 7
suqingdong
pypubmed

Toolkits for NCBI Pubmed

1K 29 8
jonatasgrosman
findpapers

Findpapers is an application that helps researchers who are looking for references for their work.

1K 343 47
HzaCode
onecite

📚 An intelligent toolkit to automatically parse, complete, and format academic references.

1K 58 8
krassowski
easy-entrez

Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.

741 81 6
twz915
pubmed

Get literature information via PubMed ID, such as the author, title, journal_name, pub_date and so on.

739 17 2
suqingdong
pubmed-xml

Pubmed XML Parser

677 4 2
synthaze
bibtools-pkg

Fetch papers and metadata.

675 5 2
suqingdong
pubmed2

search pubmeds quickly

612 6 5
dhimmel
pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

533 11 2
fphammerle
pubmed-bibtex

Generate BibTeX Entries for PubMed Publications

521 8 0
ddomingof
pubmed2pdf

A Python package to download PDFs from OA publications in PubMed

519 53 16
arundasan91
pubmed-pdf-downloader

pubmed_pdf_downloader is a Python package that allows users to bulk download PDFs of articles from PubMed Central using PMCIDs.

500 17 4
Rostlab
nalaf

NLP framework in python for entity recognition and relationship extraction

435 115 24
jakelever
pubrunner

A framework for keeping biomedical text mining result up-to-date

385 42 6
Coleridge-Initiative
richcontext-scholapi

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

367 11 3
emdb-empiar
pubmed-author-affiliation

Search for author affiliations from Pubmed for a list of Pubmed IDs and DOIs

360 1 1
jermwatt
pypmed

A Python interface for PubMed's APIs

313 5 0