📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
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Updated
May 24, 2024 - Python
📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
An R package that provides streamlined access to multiple PubMed databases, including abstracts, bibliometrics, NER annotations, and full texts.
FAIR Jupyter: a knowledge graph for semantic sharing and granular exploration of a computational notebook reproducibility dataset.
Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!
Open Access PDF harvester
Extract figures and figure captions from PMC open access papers
Citation.js plugin to output QuickStatements
ScrapeMed: Data scraping for PubMed Central.
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.
Batch downloads full-text PDFs (or any other soruces) from PubmedCentral OA articles
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.
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.
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.
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.
A library that facilitates the process of building a machine learning pipeline using PubMed as a data source
PubMed Central browser
Citation.js plugin for PubMed and PubMed Central identifiers
Extract relational tables from PubMed Central.
NLP framework in python for entity recognition and relationship extraction
This is an upgraded version of the original snorkeling project.
Add a description, image, and links to the pubmed-central topic page so that developers can more easily learn about it.
To associate your repository with the pubmed-central topic, visit your repo's landing page and select "manage topics."