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pubmed

Here are 191 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 Feb 26, 2020
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 Aug 25, 2021
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

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 Dec 1, 2021
PHP

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

EasyPubMed

naivenaive / EasyPubMed

EasyPubMed is an extension to make new PubMed easy to use

pubmed sci-hub easypubmed

Updated Sep 14, 2021

jonatasgrosman / findpapers

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

Updated Jun 22, 2021
Python

kermitt2 / biblio-glutton

A high performance bibliographic information service

doi pubmed disambiguation metadata-api openaccess bibliographical-references

Updated Dec 17, 2021
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

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 Dec 22, 2021
Java

greenelab / pubtator

Retrieve and process PubTator annotations

nlp data text-mining tool pubmed snorkel pubtator

Updated Dec 13, 2021
Python

ropensci / europepmc

R Interface to Europe PMC RESTful Web Service

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

Updated Sep 2, 2021
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

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

justinphan3110 / SciFive

SciFive: a text-text transformer model for biomedical literature

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

Updated Jun 17, 2021
Jupyter Notebook

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

PhosphorylatedRabbits / paperscraper

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

pubmed biorxiv arxiv chemrxiv medrxiv paperscraper

Updated Dec 1, 2021
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

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 Sep 17, 2021
Python

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

hetio / medline

Computing term cooccurrence in MEDLINE

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

Updated Apr 13, 2021
Jupyter Notebook

yufree / scifetch

webpage crawling tools for pubmed, google scholar and rss

rss r pubmed webcrawler google-scholar

Updated Jun 30, 2021
R

ursjoss / scipamato

Scientific Paper Management Tool

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

Updated Dec 22, 2021
Kotlin

dhimmel / delays

Sponsor

Trends in scientific publishing delays

science publishing pubmed delays publishing-delays satoshi-village

Updated Aug 20, 2021
Jupyter Notebook

esperr / search-workbench

Search Workbench is a tool for visually appraising, editing and comparing PubMed searches

pubmed information-visualization search-interface medline

Updated Apr 24, 2020
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