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 publication metadata from pubmed, arxiv, medrxiv 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

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.

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

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

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

Retrieve and process PubTator annotations

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

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

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

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)

A Python package to download full article PDFs from OA publications