pubmed

There are 289 repositories under pubmed topic.

  • ncbi-nlp/BioSentVec

    BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

    Language:Jupyter Notebook5971732100

  • ncbi-nlp/bluebert

    BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

    Language:Python578223681
  • EasyPubMed

    naivenaive/EasyPubMed

    EasyPubMed is an extension to make new PubMed easy to use

    36176144

  • jannisborn/paperscraper

    Tools to scrape publications & their metadata from pubmed, arxiv, medrxiv, biorxiv and chemrxiv.

    Language:Python334112939
  • i-librarian-free

    mkucej/i-librarian-free

    I, Librarian - open-source version of a PDF managing SaaS.

    Language:PHP30999829

  • jonatasgrosman/findpapers

    Findpapers: A tool for helping researchers who are looking for related works

    Language:Python2823935

  • AstraBert/PapersChat

    An agentic AI application that allows you to chat with your papers and gather also information from papers on ArXiv and on PubMed

    Language:Python1481015

  • kermitt2/biblio-glutton

    A high performance bibliographic information service: https://biblio-glutton.readthedocs.io

    Language:Java14486919

  • Rostlab/nalaf

    NLP framework in python for entity recognition and relationship extraction

    Language:Python1141217726

  • justinphan3110/SciFive

    SciFive: a text-text transformer model for biomedical literature

    Language:Jupyter Notebook9751916

  • 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:Python792146
  • verifAI

    nikolamilosevic86/verifAI

    VerifAI initiative to build open-source easy-to-deploy generative question-answering engine that can reference and verify answers for correctness (using posteriori model)

    Language:Jupyter Notebook763183

  • amcrisan/Adjutant

    Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents

    Language:R6891521
  • BioDEX

    KarelDO/BioDEX

    BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.

    Language:Jupyter Notebook49305

  • wcmc-its/ReCiter

    ReCiter: an enterprise open source author disambiguation system for academic institutions

    Language:Java492436726

  • hiddenblue/Pubmedsoso

    A Python mini-tool for downloading free PubMed pdf 一个批量下载pubmed免费文献的python小工具

    Language:Python47153
  • pubtrends

    JetBrains-Research/pubtrends

    Scientific literature explorer. Runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers

    Language:Python4782904

  • greenelab/pubtator

    Retrieve and process PubTator annotations

    Language:Python449139

  • IliaZenkov/async-pubmed-scraper

    PubMed scraper for async search on a list of keywords and concurrent extraction of all found URLs, returning a DataFrame/CSV containing all article data (title, abstract, authors, affiliations, etc)

    Language:Python432216

  • somewheresystems/dataclysm

    Pull high-quality, efficient embeddings for PubMed, arXiv and Wikipedia from Huggingface and use for local LLM inference/Retrieval Augmented Generation (RAG)

    Language:Jupyter Notebook43212

  • jakelever/pubrunner

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

    Language:Python42676

  • ddomingof/PubMed2PDF

    A Python package to download full article PDFs from OA publications

    Language:Python413514
  • ScrapPaper

    rafsanlab/ScrapPaper

    A web scrapping method to extract journal information from PubMed and Google Scholar using Python.

    Language:Python38235

  • nfflow/pubmedflow

    Data Collection API for pubmed

    Language:Python37236

  • tychos-ai/tychos-python

    Python library for the Tychos API. The data transformation layer for AI.

    Language:Python36207

  • dSupertramp/AItrika

    Enhance your knowledge in medical research with the help of LLM and RAG.

    Language:Python35204

  • pykong/PyperGrabber

    Fetches PubMed article IDs (PMIDs) from email inbox, then crawls PubMed, Google Scholar and Sci-Hub for respective PDF files.

    Language:Python35127

  • vgupta123/sumpubmed

    SUMPUBMED: Summarization Dataset of PubMed Scientific Article

    33123
  • pmidcite

    dvklopfenstein/pmidcite

    Download "Cited by" data from the NIH for any paper with a PubMed ID

    Language:Python325177

  • JetBrains-Research/pubtrends-review

    Automatic generation of reviews of scientific papers

    Language:Jupyter Notebook291704

  • ropensci/europepmc

    R Interface to Europe PMC RESTful Web Service

    Language:R286408

  • suqingdong/pypubmed

    Toolkits for NCBI Pubmed

    Language:Python26158

  • tychos-ai/tychos-node

    Node.js library for the Tychos API. The data transformation layer for AI.

    Language:TypeScript26204

  • christopherBelter/textmining

    Sample code and explanations for doing basic text mining tasks in R

    Language:R217011

  • mmagnus/pubmex

    get full paper names for downloaded publications automatically

    Language:Python212135

  • Zenleaf/entrez-rs

    A Rust wrapper around the Entrez API. Helps you access the Entrez API using idiomatic Rust. It also provides tools to parse the XML results from Entrez.

    Language:Rust19323