pubmed

Star

Here are 367 public repositories matching this topic...

Language:All

Filter by language

All367 Python172 Jupyter Notebook54 HTML28 R23 JavaScript13 TypeScript10 Go7 PHP7 Java6 Shell6

Sort:Most stars

Sort options

Most stars Fewest stars Most forks Fewest forks Recently updated Least recently updated

LearningCircuit /local-deep-research

Sponsor

Star3.7k

Local Deep Research achieves ~95% on SimpleQA benchmark (tested with GPT-4.1-mini). Supports local and cloud LLMs (Ollama, Google, Anthropic, ...). Searches 10+ sources - arXiv, PubMed, web, and your private documents. Everything Local & Encrypted.

home-automation encryption research local homeserver self-hosted pubmed openai brave research-tool arxiv academia mistral searxng anthropic local-llm retrieval-augmented-generation ollama deep-research local-deep-research

UpdatedDec 17, 2025
Python

ncbi-nlp /BioSentVec

Star608

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

natural-language-processing word-embeddings pubmed fasttext mimic-iii bionlp sentence-similarity sentence-embeddings sent2vec

UpdatedAug 15, 2023
Jupyter Notebook

ncbi-nlp /bluebert

Star585

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

natural-language-processing pubmed mimic-iii language-model bert pubmed-abstracts bert-model

UpdatedMar 25, 2023
Python

jannisborn /paperscraper

Star454

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

pubmed biorxiv arxiv chemrxiv medrxiv paperscraper

UpdatedDec 4, 2025
Python

naivenaive /EasyPubMed

Star398

EasyPubMed is an extension to make new PubMed easy to use

pubmed sci-hub easypubmed

UpdatedJun 21, 2025

genomoncology /biomcp

Star374

BioMCP: Biomedical Model Context Protocol

bioinformatics ai genomics mcp pubmed pubmed-central medical clinical-trials llm model-context-protocol mcp-server

UpdatedDec 15, 2025
Python

mkucej /i-librarian-free

Star319

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

php pdf ocr nasa doi saas pubmed pdf-viewer ieee groupware arxiv remote-work document-management crossref web-based research-and-development officedocs

UpdatedDec 2, 2025
PHP

jonatasgrosman /findpapers

Sponsor

Star297

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

crawler scraper research bibtex paper academic pubmed academic-publishing biorxiv ieee scopus acm arxiv papers scientific-publications scientific-papers systematic-mapping scientific-publishing systematic-review medrxiv

UpdatedFeb 5, 2024
Python

AstraBert /PapersChat

Sponsor

Star154

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

agent ai pubmed arxiv papers gradio mistral rag qdrant llm llamaindex llamaparse agentic-ai

UpdatedMay 18, 2025
Python

kermitt2 /biblio-glutton

Star146

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

doi pubmed disambiguation hal metadata-api openaccess reference-matching bibliographical-references

UpdatedJun 19, 2025
Java

Rostlab /nalaf

Star115

NLP framework in python for entity recognition and relationship extraction

python nlp ml pubmed pubmed-central pubmed-parser ner bionlp relationship-extraction

UpdatedDec 8, 2022
Python

justinphan3110 /SciFive

Star98

SciFive: a text-text transformer model for biomedical literature

nlp pubmed transformer attention flax transfer-learning pretrained-models pmc jax huggingface biomedical-language

UpdatedJun 2, 2024
Jupyter Notebook

krassowski /easy-entrez

Sponsor

Star79

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

UpdatedNov 2, 2023
Python

nikolamilosevic86 /verifAI

Sponsor

Star77

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