PyRank

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

32K 508 102
LearningCircuit
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.

24K 8K 670
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 12 9
genomoncology
biomcp-cli

BioMCP: Biomedical Model Context Protocol

4K 508 102
jannisborn
paperscraper

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

4K 517 58
cthoyt
pubmed-downloader

Automate downloading and processing PubMed in bulk

4K 6 0
suqingdong
pypubmed

Toolkits for NCBI Pubmed

1K 29 8
jonatasgrosman
findpapers

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

1K 353 48
dvklopfenstein
pmidcite

Turbocharge a PubMed literature search using citation data from the NIH

1K 34 7
twz915
pubmed

Get literature information via PubMed ID

1K 17 2
synthaze
bibtools-pkg

Fetch papers and metadata.

778 5 2
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.

714 81 6
suqingdong
pubmed-xml

Pubmed XML Parser

703 4 2
dhimmel
pubmedpy

Utilities for interacting with NCBI EUtilities relating to PubMed

639 11 2
suqingdong
pubmed2

search pubmeds quickly

615 6 5
HzaCode
onecite

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

589 59 8
Rostlab
nalaf

Natural Language Framework, for NER and RE

573 115 24
fphammerle
pubmed-bibtex

Generate BibTeX Entries for PubMed Publications

554 8 0
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.

532 18 4
ddomingof
pubmed2pdf

A Python package to download full article PDFs from OA publications

514 54 16
Coleridge-Initiative
richcontext-scholapi

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

431 11 3
emdb-empiar
pubmed-author-affiliation

Search PubMed for author affiliations of EMDB associated publications

375 1 1
nfflow
pubmedflow

Data Collection API for pubmed

319 41 8
Ferrariic
pubwords

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

278 2 0