pubmed

Local Deep Research achieves ~95% on SimpleQA benchmark (tested with GPT-4.1-mini) and includes benchmark tools to test on your own setup. Searches 10+ sources - arXiv, PubMed, GitHub, web, and your private documents. Everything Local.

BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

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

EasyPubMed is an extension to make new PubMed easy to use

I, Librarian - open-source version of a PDF managing SaaS.

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

BioMCP: Biomedical Model Context Protocol

An agentic AI application that allows you to chat with your papers and gather also information from papers on ArXiv and on PubMed

A high performance bibliographic information service: https://biblio-glutton.readthedocs.io

NLP framework in python for entity recognition and relationship extraction

SciFive: a text-text transformer model for biomedical literature

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.

VerifAI initiative to build open-source easy-to-deploy generative question-answering engine that can reference and verify answers for correctness (using posteriori model)

Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents

BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.

ReCiter: an enterprise open source author disambiguation system for academic institutions

A Python package to download full article PDFs from OA publications

A Python mini-tool for downloading free PubMed pdf 一个批量下载pubmed免费文献的python小工具

Scientific literature explorer. Runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers