Local Deep Research is an AI-powered assistant that transforms complex questions into comprehensive, cited reports by conducting iterative analysis using any LLM across diverse knowledge sources including academic databases, scientific repositories, web content, and private document collections.

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

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

EasyPubMed is an extension to make new PubMed easy to use

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

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

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

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

BioMCP: Biomedical Model Context Protocol

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.

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

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

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

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

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

Retrieve and process PubTator annotations

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)