pubmed-parser
There are 3 repositories under pubmed-parser topic.
- pubmed_parser
titipata / pubmed_parser
:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
Language:Python 586 - Language:Python 112
Tian312 / PICO_Parser
A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
Language:Python 44- ckblib
dermatologist / ckblib
Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J
Language:Java 16 nalomran / pubmed2doc
Write PubMed search results with two display options (citation or listview) to PDF or Word
Language:Python 13danielfrees / scrapemed
ScrapeMed: Data scraping for PubMed Central.
Language:Python 9Xiaowen-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 8- Language:Go 7
WengLab-InformaticsResearch / PICO_Parser
A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
Language:Python 7cakmakaf / fetch_PubMed_abstracts_by_keyword
It provides a method of how to fetch articles along with their features and text from PubMed API.
Language:Jupyter Notebook 4PubData2XL / PubData2XL
Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.
Language:HTML 4- Language:Python 4
arupgsh / PubmedScripts
Python functions to curate data from NCBI and EUROPMC API.
Language:Python 2AstraBert / 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 2- puremoe
jaytimm / puremoe
An R package that provides streamlined access to multiple PubMed databases, including abstracts, bibliometrics, NER annotations, and full texts.
Language:R 2 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:TeX 2kinleydhinata / PubMed-SyRev-Scraper
A Python tool for systematic review scraping PubMed articles based on specified search queries.
Language:Python 1LynxUtz / PubMed-parser
Parse PubMed data and get it into csv or plain text
Language:JavaScript 1michael-pagan / BIOF-309-Project
BIOF 309 Intro to Python Final Project
Language:Jupyter Notebook 1multivacplatform / multivac-pubmed
Update PubMed articles daily on HDFS by using Spark Cluster
Language:Scala 1- Language:Jupyter Notebook 1
- Language:Python 1
shriharipathak / ncbi
Crawling NCBI Pubmed Data using HTML and jQuery
Language:HTML 1Identify PICO elements and formulate Medical Evidence Propositions from clinical trial abstracts
Language:Python 1- Language:PHP 1
afnan / dxipher-js
Reference conversion library for NodeJS. Import, Export and Convert between BibTex, EndNote, XML, JSON, and more...
Language:JavaScript 0christirichards / pubmed-link-parser
Link parser for PubMed URLs using the Simple HTML DOM parser and Clipboard.js
Language:CSS 0elrf3lipes / 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!
0- Language:Java 0
MattiaCazzolla / Ehealth-project
Project from the course 'E-health methods and applications' @ Politecnico di Milano
Language:C# 0- Language:Jupyter Notebook 0
- Language:Python 0
VitalikVaseyko / Dynamic-Bernoulli-Embedding
Connecting Biological Entities From Publication Abstracts
Language:Python 0OldBonhart / EDA-NLP-PubMed-and-bioRxiv
Rapid analysis of scientific papers from bioRxiv and PubMed
Language:Jupyter Notebookrsjaffe / mendeley-medline-update
Update Mendeley keywords from medline (pubmed)
Language:Awk- Language:Python
