📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

BioMCP: Biomedical Model Context Protocol

NLP framework in python for entity recognition and relationship extraction

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.

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

Open Access PDF harvester

A tool for harvesting media files from Open Access articles for upload into Wikimedia Commons

ScrapeMed: Data scraping for PubMed Central.

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

Bash scripts to bulk download full-text PDFs (or any other soruces) from PubmedCentral OA articles

MediaWiki bot to upload content to Wikimedia projects and update corresponding citations on Wikipedia.

Repository of our paper on Self-citation analysis in PubMed data

The aim of this project is to use the text from biomedical and life science literature to gain insights on research topic trends over time.

A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale

Citation.js plugin to output QuickStatements

This script reads the exported (.csv|.txt) files from Scopus, Web of Science, PubMed, PubMed Central, Dimensions or Google Scholar exported from Publish or Perish databases and turns each of them into a new file with an unique format. This script will ignore duplicated records.

A library that facilitates the process of building a machine learning pipeline using PubMed as a data source

Extract figures and figure captions from PMC open access papers

PubMed Central browser

This is an upgraded version of the original snorkeling project.