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

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

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

Tools to scrape publication metadata from pubmed, arxiv, medrxiv and chemrxiv.

NLP framework in python for entity recognition and relationship extraction

A high performance bibliographic information service

SciFive: a text-text transformer model for biomedical literature

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

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.

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

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

Retrieve and process PubTator annotations

Python library for the Tychos API. The data transformation layer for AI.

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

A Python package to download full article PDFs from OA publications

Data Collection API for pubmed

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

A web scrapping method to extract journal information from PubMed and Google Scholar using Python.