titipata/pubmed_parser

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

Language: Python - Size: 60.4 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 643 - Forks: 171

AstraBert/BioMedicalPapersBot

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

Language: Python - Size: 321 KB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 3 - Forks: 1

Rostlab/nalaf

NLP framework in python for entity recognition and relationship extraction

Language: Python - Size: 32 MB - Last synced at: 9 days ago - Pushed at: over 2 years ago - Stars: 114 - Forks: 26

jaytimm/puremoe

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

Language: R - Size: 4.21 MB - Last synced at: 14 days ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

suqingdong/pubmed_xml

PubMed XML Parser

Language: Python - Size: 18.6 KB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

kinleydhinata/PubMed-SyRev-Scraper

A Python tool for systematic review scraping PubMed articles based on specified search queries.

Language: Python - Size: 29.3 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

dermatologist/ckblib

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

Language: Java - Size: 970 KB - Last synced at: 10 days ago - Pushed at: 10 months ago - Stars: 16 - Forks: 4

elrf3lipes/ramon-s_portfolio

I'm passionate about Cloud and DevOps, and for the moment I'm posting some of my work and personal projects here to showcase that. If its useful for you, feel free to integrate or contribute!

Size: 915 KB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

PubData2XL/PubData2XL

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

Language: HTML - Size: 6.37 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 1

danielfrees/scrapemed

ScrapeMed: Data scraping for PubMed Central.

Language: Python - Size: 13.6 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

ninnii55/YAPPP

Yet Another PubMed Python Parser

Language: Jupyter Notebook - Size: 1.24 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

zakcali/pubmedapi

get document info from pubmedapi if PMID is known

Language: PHP - Size: 99.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

hscells/transmute

PubMed/Medline query transpiler

Language: Go - Size: 816 KB - Last synced at: 17 days ago - Pushed at: over 5 years ago - Stars: 7 - Forks: 2

shreyas1701/Pubmed-PMC-Parser

Language: Python - Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

Xiaowen-JI/Semi-automation-of-systematic-review-of-clinical-trials-in-medical-psychology-with-BERT-models

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 F1, precision, and recall increasing to 0.95, 0.94, and 0.96 respectively. Training sample size of 100 results in the most cost-effective performance.

Language: Jupyter Notebook - Size: 4.7 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1

jacons/CHL-Project

Computational Health Laboratory project

Language: Jupyter Notebook - Size: 14.7 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

samiullah/pubmed_parser

Pubmed Parser to get author emails in csv

Language: Python - Size: 6.9 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

MattiaCazzolla/Ehealth-project

Project from the course 'E-health methods and applications' @ Politecnico di Milano

Language: C# - Size: 202 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

Kero76/fdd 📦

Data mining repository

Language: Java - Size: 55.3 MB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

WengLab-InformaticsResearch/PICO_Parser

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

Language: Python - Size: 194 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 1

LynxUtz/PubMed-parser

Parse PubMed data and get it into csv or plain text

Language: JavaScript - Size: 85 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

arupgsh/PubmedScripts

Python functions to curate data from NCBI and EUROPMC API.

Language: Python - Size: 113 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

multivacplatform/multivac-pubmed

Update PubMed articles daily on HDFS by using Spark Cluster

Language: Scala - Size: 30.3 KB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

matteotolloso/BioCograph

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

Language: Python - Size: 102 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

afnan/dxipher-js Fork of summonr/reference-js

Reference conversion library for NodeJS. Import, Export and Convert between BibTex, EndNote, XML, JSON, and more...

Language: JavaScript - Size: 437 KB - Last synced at: 9 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

nalomran/pubmed2doc

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

Language: Python - Size: 269 KB - Last synced at: 18 days ago - Pushed at: over 4 years ago - Stars: 13 - Forks: 2

it21208/Experiments-with-CLEF-and-TREC-CommonCore

Some Python scripts and Java classes to make several open source toolkits to work with CLEF (PubMed docs) and TREC Common Core datasets. The code developed aimed to improve document classification by exploring some pretrained word embeddings like BERT and PubMedBERT and to investigate a Semantic search approach incorporating the Sentence-BERT model for both datasets.

Language: Python - Size: 269 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

OldBonhart/EDA-NLP-PubMed-and-bioRxiv

Rapid analysis of scientific papers from bioRxiv and PubMed

Language: Jupyter Notebook - Size: 324 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

natc79/PubMed

Download and process documents from PubMed

Language: Jupyter Notebook - Size: 1.04 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 2

tobias76/BioParser

Simple PubMed XML Parser

Language: Python - Size: 7.81 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

michael-pagan/BIOF-309-Project

BIOF 309 Intro to Python Final Project

Language: Jupyter Notebook - Size: 223 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

hashemi/refparser

Python 3 library for parsing academic references in RIS or MEDLINE formats

Language: Python - Size: 139 KB - Last synced at: 3 days ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1

rsjaffe/mendeley-medline-update

Update Mendeley keywords from medline (pubmed)

Language: Awk - Size: 17.6 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

shriharipathak/ncbi

Crawling NCBI Pubmed Data using HTML and jQuery

Language: HTML - Size: 77.1 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

christirichards/pubmed-link-parser

Link parser for PubMed URLs using the Simple HTML DOM parser and Clipboard.js

Language: CSS - Size: 2.15 MB - Last synced at: 3 days ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0