#

pubmed

Here are 203 public repositories matching this topic...

ncbi-nlp / BioSentVec

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

Updated Jan 12, 2022
Jupyter Notebook

ncbi-nlp / bluebert

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

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

Updated May 26, 2022
Python

Rostlab / nalaf

NLP framework in python for entity recognition and relationship extraction

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

Updated Nov 9, 2021
Python

EasyPubMed

naivenaive / EasyPubMed

EasyPubMed is an extension to make new PubMed easy to use

pubmed sci-hub easypubmed

Updated Jun 2, 2022

i-librarian-free

mkucej / i-librarian-free

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

Updated May 26, 2022
PHP

jonatasgrosman / findpapers

Sponsor

Findpapers is an application that helps researchers who are looking for references for their work

Updated Jun 1, 2022
Python

amcrisan / Adjutant

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

text-mining r shiny pubmed summaries

Updated Mar 18, 2020
R

kermitt2 / biblio-glutton

A high performance bibliographic information service

doi pubmed disambiguation metadata-api openaccess bibliographical-references

Updated Apr 27, 2022
Java

jakelever / pubrunner

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

python infrastructure text-mining snakemake pubmed pubmed-central bionlp

Updated Jul 11, 2020
Python

justinphan3110 / SciFive

SciFive: a text-text transformer model for biomedical literature

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

Updated Apr 9, 2022
Jupyter Notebook

greenelab / pubtator

Retrieve and process PubTator annotations

nlp data text-mining tool pubmed snorkel pubtator

Updated Jan 3, 2022
Python

wcmc-its / ReCiter

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

java aws algorithm spring-boot maven clustering dynamodb machine-learning-algorithms entity-resolution s3 pubmed scopus reciter elasticbeanstalk awscodebuild awscodepipeline

Updated Apr 6, 2022
Java

ropensci / europepmc

R Interface to Europe PMC RESTful Web Service

r pubmed rstats r-package scientific-publications bibliometrics europe-pmc scientific-literature pubmedcentral

Updated Jan 16, 2022
R

christopherBelter / textmining

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

api text-mining r pubmed topic-modeling

Updated Sep 2, 2020
R

JetBrains-Research / pubtrends-review

Automatic generation of reviews of scientific papers

natural-language-processing deep-learning pubmed extractive-summarization

Updated Nov 3, 2021
Jupyter Notebook

PhosphorylatedRabbits / paperscraper

Tools to scrape publication metadata from pubmed, arxiv, medrxiv and chemrxiv.

pubmed biorxiv arxiv chemrxiv medrxiv paperscraper

Updated Apr 19, 2022
Python

pykong / PyperGrabber

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

python pdf crawler scraper pubmed pmid google-scholar sci-hub email-inbox

Updated Oct 23, 2018
Python

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.

pubmed pubmed-central entrez meta-analysis gene-annotations literature-mining eutilities literature-search entrez-eutilities

Updated Jan 29, 2022
Python

lukeholman / genderGapCode

Code used to extract and analyse gender data from PubMed and arXiv in 2018 PLOS Biol paper

text-mining pubmed arxiv gender-classification

Updated Jul 5, 2019
R

ddomingof / PubMed2PDF

A Python package to download full article PDFs from OA publications

pdf pubmed open-access scientific-publications articles-google-scholar scientific-literature

Updated Jul 19, 2021
Python

twz915 / pubmed

Get literature information via PubMed ID, such as the author, title, journal_name, pub_date and so on.

journal reference pubmed literature

Updated Sep 11, 2016
Python

nalomran / pubmed2doc

Write PubMed search results with two display options (citation or listview) to PDF or Word

bioinformatics python3 pubmed pubmed-parser biopython docx fpdf

Updated Oct 18, 2020
Python

hetio / medline

Computing term cooccurrence in MEDLINE

text-mining pubmed rephetio hetionet literature diseases medline cooccurrence symptoms anatomy

Updated Apr 13, 2021
Jupyter Notebook

hclent / Science-Citation-Knowledge-Extractor

A web tool that helps biomedical researchers understand how their work is being used by others, by analyzing the content in papers that cite them

flask machine-learning natural-language-processing data-visualization python3 pubmed

Updated Oct 19, 2018
HTML

NCBI-Hackathons / phenotypeXpression

Subclassification of disease states based on the intersection of literature and expression

rna-seq pubmed ncbi ncbi-geo precision-medicine

Updated Jan 15, 2019
Python

christopherBelter / pubmedXML

Parse PubMed XML into a data frame in R

r parsing xml pubmed extract-xml

Updated May 2, 2021
R

yufree / scifetch

webpage crawling tools for pubmed, google scholar and rss

rss r pubmed webcrawler google-scholar

Updated Jun 30, 2021
R

suqingdong / pypubmed

Toolkits for NCBI Pubmed

pubmed ncbi sci

Updated Aug 11, 2021
Python

Imamachi-n / BioRxivCurator

Batch scripts curating BioRxiv and PubMed articles by using Altmetric score.

slack raspberry-pi twitter-bot pubmed biorxiv slack-bot altmetrics-data

Updated May 9, 2020
Python

ursjoss / scipamato

Scientific Paper Management Tool

spring-boot pubmed scientific-journals jooq wicket-framework swisstph ludok

Updated May 28, 2022
Kotlin

Improve this page

Add a description, image, and links to the pubmed topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with the pubmed topic, visit your repo's landing page and select "manage topics."