Ecosyste.ms: Repos

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GitHub topics: pubmed-parser

Repositories

jaytimm/puremoe

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

Language: R - Size: 1000 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 0

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: 18 days ago - Pushed: 18 days ago - Stars: 551 - Forks: 164

PubData2XL/PubData2XL

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

Language: HTML - Size: 6.22 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 2 - Forks: 0

gauravcodepro/pubmed-abstract-fetcher

This function will prepare the abstract and the id information for all the pubmed articles that you want to read and have as a citation. I coded this using a web scraping approach and it is blazing fast and parses better than ncbi eutils

Language: Python - Size: 27.3 KB - Last synced: 27 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

danielfrees/scrapemed

ScrapeMed: Data scraping for PubMed Central.

Language: Python - Size: 13.6 MB - Last synced: 28 days ago - Pushed: 5 months ago - Stars: 4 - Forks: 1

suqingdong/pubmed_xml

PubMed XML Parser

Language: Python - Size: 15.6 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 4 - Forks: 2

ninnii55/YAPPP

Yet Another PubMed Python Parser

Language: Jupyter Notebook - Size: 1.24 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

hashemi/refparser

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

Language: Python - Size: 139 KB - Last synced: 3 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

Rostlab/nalaf

NLP framework in python for entity recognition and relationship extraction

Language: Python - Size: 32 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 111 - Forks: 26

dermatologist/ckblib

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

Language: Java - Size: 875 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 14 - Forks: 4

nalomran/pubmed2doc

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

Language: Python - Size: 269 KB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 13 - Forks: 3

zakcali/pubmedapi

get document info from pubmedapi if PMID is known

Language: PHP - Size: 99.6 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

hscells/transmute

PubMed/Medline query transpiler

Language: Go - Size: 816 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 7 - Forks: 2

shreyas1701/Pubmed-PMC-Parser

Language: Python - Size: 7.81 KB - Last synced: 10 months ago - Pushed: over 6 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: 12 months ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 1

jacons/CHL-Project

Computational Health Laboratory project

Language: Jupyter Notebook - Size: 14.7 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

samiullah/pubmed_parser

Pubmed Parser to get author emails in csv

Language: Python - Size: 6.9 MB - Last synced: about 1 year ago - Pushed: over 5 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: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Kero76/fdd 📦

Data mining repository

Language: Java - Size: 55.3 MB - Last synced: over 1 year ago - Pushed: over 6 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: about 1 year ago - Pushed: about 4 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: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

arupgsh/PubmedScripts

Python functions to curate data from NCBI and EUROPMC API.

Language: Python - Size: 113 KB - Last synced: 8 months ago - Pushed: about 3 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: over 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

afnan/dxipher-js Fork of Natedeploys/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: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

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: about 1 year ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0