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

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

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

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

ScrapeMed: Data scraping for PubMed Central.

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.

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

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

Citation.js plugin to output QuickStatements

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

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

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.

Extract figures and figure captions from PMC open access papers

This is an upgraded version of the original snorkeling project.

Citation.js plugin for PubMed and PubMed Central identifiers

PubMed Central browser