Local Deep Research achieves ~95% on SimpleQA benchmark (tested with GPT-4.1-mini). Supports local and cloud LLMs (Ollama, Google, Anthropic, ...). Searches 10+ sources - arXiv, PubMed, web, and your private documents. Everything Local & Encrypted.

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.

BioMCP: Biomedical Model Context Protocol

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

AI-Powered Bioinformatics Research Assistant. Built on OpenClaw.

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

A Node.js implementation of the Model Context Protocol (MCP) server for searching and downloading academic papers from multiple sources, including **Web of Science**, arXiv, and more.

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)

An MCP server that provides comprehensive medical information by querying multiple authoritative medical APIs including FDA, WHO, PubMed, Google Scholar, and RxNorm

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

MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata, generate citations, explore MeSH terms, and discover related research. Runs over stdio or HTTP. Deployable to Cloudflare Workers.

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

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

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

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

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

Pull high-quality, efficient embeddings for PubMed, arXiv and Wikipedia from Huggingface and use for local LLM inference/Retrieval Augmented Generation (RAG)

Retrieve and process PubTator annotations

PubMed scraper for async search on a list of keywords and concurrent extraction of all found URLs, returning a DataFrame/CSV containing all article data (title, abstract, authors, affiliations, etc)

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

Data Collection API for pubmed