pubmed
There are 261 repositories under pubmed topic.
ncbi-nlp/BioSentVec
BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences
ncbi-nlp/bluebert
BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).
naivenaive/EasyPubMed
EasyPubMed is an extension to make new PubMed easy to use
mkucej/i-librarian-free
I, Librarian - open-source version of a PDF managing SaaS.
jonatasgrosman/findpapers
Findpapers: A tool for helping researchers who are looking for related works
jannisborn/paperscraper
Tools to scrape publication metadata from pubmed, arxiv, medrxiv and chemrxiv.
kermitt2/biblio-glutton
A high performance bibliographic information service: https://biblio-glutton.readthedocs.io
Rostlab/nalaf
NLP framework in python for entity recognition and relationship extraction
justinphan3110/SciFive
SciFive: a text-text transformer model for biomedical literature
amcrisan/Adjutant
Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents
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.
wcmc-its/ReCiter
ReCiter: an enterprise open source author disambiguation system for academic institutions
jakelever/pubrunner
A framework for keeping biomedical text mining result up-to-date
greenelab/pubtator
Retrieve and process PubTator annotations
KarelDO/BioDEX
BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.
tychos-ai/tychos-python
Python library for the Tychos API. The data transformation layer for AI.
JetBrains-Research/pubtrends
Scientific literature explorer. Runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers
ddomingof/PubMed2PDF
A Python package to download full article PDFs from OA publications
nfflow/pubmedflow
Data Collection API for pubmed
somewheresystems/dataclysm
Pull high-quality, efficient embeddings for PubMed, arXiv and Wikipedia from Huggingface and use for local LLM inference/Retrieval Augmented Generation (RAG)
rafsanlab/ScrapPaper
A web scrapping method to extract journal information from PubMed and Google Scholar using Python.
JetBrains-Research/pubtrends-review
Automatic generation of reviews of scientific papers
pykong/PyperGrabber
Fetches PubMed article IDs (PMIDs) from email inbox, then crawls PubMed, Google Scholar and Sci-Hub for respective PDF files.
dvklopfenstein/pmidcite
Turbocharge a PubMed literature rather than clicking and clicking and clicking on Google Scholar
ropensci/europepmc
R Interface to Europe PMC RESTful Web Service
tychos-ai/tychos-node
Node.js library for the Tychos API. The data transformation layer for AI.
vgupta123/sumpubmed
SUMPUBMED: Summarization Dataset of PubMed Scientific Article
suqingdong/pypubmed
Toolkits for NCBI Pubmed
hiddenblue/Pubmedsoso
一个批量下载pubmed免费文献的python小工具
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)
dSupertramp/AItrika
Enhance your knowledge in medical research with the help of LLM and RAG.
christopherBelter/textmining
Sample code and explanations for doing basic text mining tasks in R
mmagnus/pubmex
get full paper names for downloaded publications automatically
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.
lukeholman/genderGapCode
Code used to extract and analyse gender data from PubMed and arXiv in 2018 PLOS Biol paper
twz915/pubmed
Get literature information via PubMed ID, such as the author, title, journal_name, pub_date and so on.