pubmed-central

There are 3 repositories under pubmed-central topic.

• pubmed_parser

  titipata / pubmed_parser

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

  pythonpubmed-centralpubmed-parserparsexmlmedline-xmlarticlenlpdoipmidparser
  Language:Python 548

• Rostlab / nalaf

  NLP framework in python for entity recognition and relationship extraction

  nlpbionlprelationship-extractionnermlpythonpubmedpubmed-parserpubmed-central
  Language:Python 112

• 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.

  entrezpubmedliterature-searchliterature-miningentrez-eutilitieseutilitiespubmed-centralgene-annotationsmeta-analysis
  Language:Python 61

• jakelever / pubrunner

  A framework for keeping biomedical text mining result up-to-date

  bionlptext-mininginfrastructurepythonsnakemakepubmedpubmed-central
  Language:Python 41

• kermitt2 / biblio_glutton_harvester

  Open Access PDF harvester

  openaccesspdfharvesters3-storagepubmed-centralunpaywallswift-storage
  Language:Python 32

• wpoa / open-access-media-importer

  A tool for harvesting media files from Open Access articles for upload into Wikimedia Commons

  open-accesspubmed-centralmultimediavideoaudiopywikibotpythonwikimedia-commons
  Language:Python 23

• jakelever / biotext

  Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

  biocpubmedpubmed-centralpubtatorsnakemaketext-mining
  Language:Python 13

• 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.

  life-science-literaturedynamic-topic-modelingpubmed-centraltext-miningtopic-modeling
  Language:Jupyter Notebook 9

• wpoa / recitation-bot

  MediaWiki bot to upload content to Wikimedia projects and update corresponding citations on Wikipedia.

  pywikibotmediawiki-botpythondoipubmed-centralwikisourcewikimedia-commonsopen-access
  Language:Python 9

• napsternxg / PubMed_SelfCitationAnalysis

  Repository of our paper on Self-citation analysis in PubMed data

  pubmed-centralcitation-analysismedlineregression-modelsspark
  Language:Jupyter Notebook 8

• tiadams / pmc-downloader

  Batch downloads full-text PDFs (or any other soruces) from PubmedCentral OA articles

  pdfxmlpmcidpmcpubmed-centralpubmedbash-scriptshellcurl
  Language:Shell 8

• NCBI-Hackathons / Hidden-Figures

  A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale

  nlppubmedpubmed-centralgender-recognitionanalysispythonhackathon
  Language:Jupyter Notebook 7

• citation-js / plugin-quickstatements

  Citation.js plugin to output QuickStatements

  wikidataquickstatementspubmedpubmed-centraldoicrossrefcitation-js
  Language:JavaScript 6

• nicford / Pubmed-Pipeline

  A library that facilitates the process of building a machine learning pipeline using PubMed as a data source

  pubmedpipelinemachine-learningncbinlmxmlpysparklibrarypubmed-central
  Language:Python 5

• danielfrees / scrapemed

  ScrapeMed: Data scraping for PubMed Central.

  datadata-sciencedata-scraperembeddingsmedical-datapubmedpubmed-centralpubmed-parserpythonscrapingscraping-pythonscrapemed
  Language:Python 4

• etowahadams / PMC-figure-downloader

  Extract figures and figure captions from PMC open access papers

  bioinformaticsentrezpubmed-centralpubmed
  Language:Jupyter Notebook 4

• greenelab / snorkeling-full-text

  This is an upgraded version of the original snorkeling project.

  natural-language-processingtext-miningpubmed-centralmachine-learning
  Language:Jupyter Notebook 4

• citation-js / plugin-pubmed

  Citation.js plugin for PubMed and PubMed Central identifiers

  pubmed-identifierspubmedpubmed-centralcitation-js
  Language:JavaScript 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.

  dimensionsgoogle-scholarpublish-or-perishpubmedpubmed-centralscopussystematic-reviewweb-of-science
  Language:Python 3

• dualword / dualword-pmc

  PubMed Central browser

  pubmedpubmed-centralpdftext-miningcppfull-text-searchmedical-educationmedical-informaticsmedical-informationmedicalscientific-papersbiomedicalscientific-publicationsmedicinepdfiumsqlitexapianqt5site-specific-browsercross-platform
  Language:C++ 2

• FAIR-ethics / PMC-ethics

  observations about ethical aspects of publications available via PubMed Central

  ethicsfairpubmed-central
  2

• 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.

  dimensionsgoogle-scholarpublish-or-perishpubmedpubmed-centralscopussystematic-reviewweb-of-science
  Language:Python 2

• RohitChattopadhyay / ihop-reach

  API https://reach-api.nrnb-docker.ucsd.edu WebApp https://reach.nrnb-docker.ucsd.edu

  bioinformaticsgatsbyjsgraphqlgsoc-2019pubmed-central
  2

• clulab / edin-data

  Biomolecular events mined by Reach from PubMed Central

  information-extractionpubmed-centralnlp-datasets
  1

• fusion-jena / fairjupyter

  FAIR Jupyter: a knowledge graph for semantic sharing and granular exploration of a computational notebook reproducibility dataset.

  fair-datajupyter-notebookknowledge-graphontologypubmed-centralpythonreproducibility
  Language:Shell 1

• 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.

  dimensionsgoogle-scholarpublish-or-perishpubmedpubmed-centralscopussystematic-reviewweb-of-science
  Language:Python 1

• 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.

  dimensionsgoogle-scholarpubmedpubmed-centralscopussystematic-reviewweb-of-sciencepublish-or-perish
  Language:Python 1
• puremoe

  jaytimm / puremoe

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

  pubmed-centralpubmed-parser
  Language:R 1

• pmc-tables / pmc-tables

  Extract relational tables from PubMed Central.

  pmc-tablespubmed-centralextract-tables
  Language:Jupyter Notebook 1

• nancyshaji / PubMedFullText

  Provides link of the full-text article upon giving PubMed's PMID

  pubmed-recordspubmedpmidbeautifulsouppubmed-articlespubmed-centralpython3webscraping
  Language:Python 0