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

NLP framework in python for entity recognition and relationship extraction

A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework

Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J

Write PubMed search results with two display options (citation or listview) to PDF or Word

ScrapeMed: Data scraping for PubMed Central.

We employed pre-trained BERT models (distillBERT, BioBert, and SciBert) for text-classifications of the titles and abstracts of clinical trials in medical psychology. The average score of AUC is 0.92. A stacked model was then built by featuring the probability predicted by distillBERT and keywords of search domains. The AUC improved to 0.96 with…

PubMed/Medline query transpiler

A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework

Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.

It provides a method of how to fetch articles along with their features and text from PubMed API.

PubMed XML Parser

Python functions to curate data from NCBI and EUROPMC API.

An R package that provides streamlined access to multiple PubMed databases, including abstracts, bibliometrics, NER annotations, and full texts.

A tool capable of parsing datasets of papers from pubmed, annotating entities that appear using bio-BERT, creating a network of cooccurrences on which to perform analysis with various algorithms

A Gradio bot to retrieve PubMed papers' title, doi, authors and publication date based on general search terms or on specific publication names

BIOF 309 Intro to Python Final Project

Pubmed Parser to get author emails in csv

Download and process documents from PubMed

Identify PICO elements and formulate Medical Evidence Propositions from clinical trial abstracts