📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
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Jul 31, 2025 - Python
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pubmed-central
Here are 44 public repositories matching this topic...
BioMCP: Biomedical Model Context Protocol
bioinformatics ai genomics mcp pubmed pubmed-central medical clinical-trials llm model-context-protocol mcp-server
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Aug 11, 2026 - Rust
NLP framework in python for entity recognition and relationship extraction
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Dec 8, 2022 - Python
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.
pubmed pubmed-central entrez meta-analysis gene-annotations literature-mining eutilities literature-search entrez-eutilities
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Nov 2, 2023 - Python
Open Access PDF harvester
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May 3, 2024 - Python
A framework for keeping biomedical text mining result up-to-date
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Jul 11, 2020 - Python
A tool for harvesting media files from Open Access articles for upload into Wikimedia Commons
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Jul 3, 2016 - Python
A PMC ID in. Clean, loss-aware article JSON out. Parse PubMed Central and JATS XML for biomedical AI, RAG, search, and literature pipelines.
python text-mining bioinformatics pubmed open-science pubmed-central knowledge-graph xml-parser jats jats-xml pmc rag scientific-literature llm biomedical-nlp biomedical-ai
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Aug 3, 2026 - Python
ScrapeMed: Data scraping for PubMed Central.
python data-science data scraping pubmed embeddings pubmed-central pubmed-parser data-scraper medical-data scraping-python scrapemed
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Jan 6, 2024 - Python
Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!
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Jun 10, 2024 - Python
Bash scripts to bulk download full-text PDFs (or any other sources) from PubmedCentral OA articles
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May 8, 2026 - Shell
MediaWiki bot to upload content to Wikimedia projects and update corresponding citations on Wikipedia.
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Mar 19, 2021 - Python
A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale
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Jan 20, 2019 - Jupyter Notebook
Repository of our paper on Self-citation analysis in PubMed data
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Apr 25, 2018 - Jupyter Notebook
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.
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Sep 20, 2017 - Jupyter Notebook
MedPMC: a high-fidelity medical image–text curation framework from biomedical literature for multimodal foundation models, with released pipelines, curated data, benchmarks, and pretrained models.
pubmed-central medical-imaging reproducibility medical-ai biomedical-literature foundation-models dataset-curation vision-language-model multimodal-ai
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Jul 19, 2026 - Python
Citation.js plugin to output QuickStatements
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Dec 2, 2025 - JavaScript
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.
dimensions pubmed pubmed-central scopus google-scholar web-of-science systematic-review publish-or-perish
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May 30, 2025
A library that facilitates the process of building a machine learning pipeline using PubMed as a data source
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Jul 6, 2023 - Python
Extract figures and figure captions from PMC open access papers
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Apr 3, 2024 - Jupyter Notebook
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