Topic: "pubmed-central"
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: 1 day ago - Pushed at: about 2 months ago - Stars: 683 - Forks: 175
genomoncology/biomcp
BioMCP: Biomedical Model Context Protocol
Language: Python - Size: 5.4 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 212 - Forks: 28
Rostlab/nalaf
NLP framework in python for entity recognition and relationship extraction
Language: Python - Size: 32 MB - Last synced at: 26 days ago - Pushed at: over 2 years ago - Stars: 115 - Forks: 26
krassowski/easy-entrez
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.
Language: Python - Size: 120 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 79 - Forks: 6
jakelever/pubrunner
A framework for keeping biomedical text mining result up-to-date
Language: Python - Size: 565 KB - Last synced at: about 22 hours ago - Pushed at: about 5 years ago - Stars: 42 - Forks: 6
kermitt2/biblio_glutton_harvester
Open Access PDF harvester
Language: Python - Size: 509 KB - Last synced at: 6 days ago - Pushed at: about 1 year ago - Stars: 40 - Forks: 5
wpoa/open-access-media-importer Fork of RaphaelWimmer/open-access-media-importer
A tool for harvesting media files from Open Access articles for upload into Wikimedia Commons
Language: Python - Size: 1.24 MB - Last synced at: 12 months ago - Pushed at: about 9 years ago - Stars: 23 - Forks: 8
jakelever/biotext
Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!
Language: Python - Size: 382 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 5
wpoa/recitation-bot
MediaWiki bot to upload content to Wikimedia projects and update corresponding citations on Wikipedia.
Language: Python - Size: 149 KB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 3
napsternxg/PubMed_SelfCitationAnalysis
Repository of our paper on Self-citation analysis in PubMed data
Language: Jupyter Notebook - Size: 17.6 MB - Last synced at: 3 months ago - Pushed at: about 7 years ago - Stars: 8 - Forks: 1
Ailuropoda1864/PMC-text-mining
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.
Language: Jupyter Notebook - Size: 20.5 MB - Last synced at: over 2 years ago - Pushed at: almost 8 years ago - Stars: 8 - Forks: 2
citation-js/plugin-quickstatements
Citation.js plugin to output QuickStatements
Language: JavaScript - Size: 87.9 KB - Last synced at: 20 days ago - Pushed at: 2 months ago - Stars: 7 - Forks: 2
NCBI-Hackathons/Hidden-Figures
A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale
Language: Jupyter Notebook - Size: 30.9 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 3
LBMCF/format-input
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.
Size: 95.7 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 0
tiadams/pmc-downloader
Downloads full-text PDFs (or any other soruces) from PubmedCentral OA articles
Language: Shell - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1
etowahadams/PMC-figure-downloader
Extract figures and figure captions from PMC open access papers
Language: Jupyter Notebook - Size: 29.3 KB - Last synced at: 1 day ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0
danielfrees/scrapemed
ScrapeMed: Data scraping for PubMed Central.
Language: Python - Size: 13.6 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1
greenelab/snorkeling-full-text
This is an upgraded version of the original snorkeling project.
Language: Jupyter Notebook - Size: 113 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 1
nicford/Pubmed-Pipeline
A library that facilitates the process of building a machine learning pipeline using PubMed as a data source
Language: Python - Size: 67.4 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 1
LBMCF/remove-duplicates
This script eliminates the duplicated records from formatted .xlsx files from Scopus, Web of Science, PubMed, PubMed Central, Dimensions or Google Scholar exported from Publish or Perish. Is mandatory that there be at least 2 different files from 2 different databases.
Size: 85.9 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0
glenjasper/remove-duplicates
This script eliminates the duplicated records from formatted .xlsx files from Scopus, Web of Science, PubMed, PubMed Central, Dimensions or Google Scholar exported from Publish or Perish. Is mandatory that there be at least 2 different files from 2 different databases.
Language: Python - Size: 61.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0
glenjasper/format-input
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.
Language: Python - Size: 51.8 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0
osl-incubator/pymedx Fork of gijswobben/pymed
PyMedX is a Python library that provides access to PubMed.
Language: Python - Size: 1.39 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 3
citation-js/plugin-pubmed
Citation.js plugin for PubMed and PubMed Central identifiers
Language: JavaScript - Size: 18.6 KB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0
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: about 8 hours ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0
fusion-jena/fairjupyter
FAIR Jupyter: a knowledge graph for semantic sharing and granular exploration of a computational notebook reproducibility dataset.
Language: Jupyter Notebook - Size: 16.9 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0
dualword/dualword-pmc
PubMed Central browser
Language: C++ - Size: 2.04 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
RohitChattopadhyay/ihop-reach Fork of cannin/ihop-reach
API https://reach-api.nrnb-docker.ucsd.edu WebApp https://reach.nrnb-docker.ucsd.edu
Size: 700 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1
pmc-tables/pmc-tables
Extract relational tables from PubMed Central.
Language: Jupyter Notebook - Size: 3.55 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
clulab/edin-data
Biomolecular events mined by Reach from PubMed Central
Size: 3.29 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1
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: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
