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pubmed

Here are 141 public repositories matching this topic...

ncbi-nlp / BioSentVec

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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

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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 Jun 9, 2020
Python

Rostlab / nalaf

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Open

Delete Output Formats wiki page ?

2

juanmirocks commented Dec 9, 2015

Wiki page: https://github.com/Rostlab/nalaf/wiki/Output-Formats
Confirm if you still use the simple JSON export
- if yes:
  - fix documentation of format (I guess it's wrong because I guess each document should be an array of parts
  - Link wiki page link to Home wiki
  - Support output format in example & nala scripts
- else:
  - delete that wiki page since

Read more

Open

Change the way features are saved

4

amcrisan / Adjutant

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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

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A high performance bibliographic information service

doi pubmed disambiguation metadata-api openaccess bibliographical-references

Updated Jun 5, 2020
Java

jakelever / pubrunner

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

python infrastructure text-mining snakemake pubmed pubmed-central bionlp

Updated May 6, 2020
Python

wcmc-its / ReCiter

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Open

Audit log in Gold Standard table not indicating the person who made the change

paulalbert1 commented Dec 18, 2018

For example, in this case, I (paa2013) made the change. Instead, it would appear Dikoma Shungu did (which is inaccurate).

This information will be useful for reporting purposes.

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enhancement

mkucej / i-librarian-free

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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 Jul 5, 2020
PHP

ropensci / europepmc

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R Interface to Europe PMC RESTful Web Service

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

Updated Jun 5, 2020
R

christopherBelter / textmining

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

api text-mining r pubmed topic-modeling

Updated Nov 6, 2019
R

twz915 / pubmed

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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

greenelab / pubtator

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Retrieve and process PubTator annotations

nlp data text-mining pubmed snorkel pubtator

Updated Mar 2, 2020
Python

lukeholman / genderGapCode

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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

pykong / PyperGrabber

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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

NCBI-Hackathons / phenotypeXpression

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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

hclent / Science-Citation-Knowledge-Extractor

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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

ursjoss / scipamato

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Scientific Paper Management Tool

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

Updated Jul 5, 2020
Java

ddomingof / PubMed2PDF

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A Python package to download full article PDFs from OA publications

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

Updated Jul 18, 2019
Python

esperr / search-workbench

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

pubmed information-visualization search-interface medline

Updated Apr 24, 2020
JavaScript

Imamachi-n / BioRxivCurator

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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

dhimmel / delays

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Trends in scientific publishing delays

science publishing pubmed delays publishing-delays satoshi-village

Updated Mar 20, 2017
Jupyter Notebook

hscells / groove

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Query analysis pipeline framework

framework pipeline analysis pubmed qpp medline elaticsearch boolean-query

Updated Apr 8, 2020
Go

christopherBelter / pubmedXML

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Parse PubMed XML into a data frame in R

r parsing xml pubmed extract-xml

Updated Mar 28, 2019
R

Quiltomics / godseye

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Monitor biomedical trends visually across ALL of PubMed + bioRxiv

visualization python text-mining bioinformatics computational-biology pubmed biorxiv

Updated Oct 23, 2018
Python

yufree / scifetch

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webpage crawling tools for pubmed, google scholar and rss

rss r pubmed webcrawler google-scholar

Updated Feb 28, 2020
R

uludag / nosql-biosets

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index and query scripts for free reference bioinformatics datasets

bioinformatics pubmed hgnc drugbank uniprot clinvar hmdb intenz metanetx

Updated Jul 5, 2020
Python

dhimmel / medline

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Computing term cooccurrence in MEDLINE

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

Updated Mar 28, 2016
Jupyter Notebook

NCBI-Hackathons / Hidden-Figures

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A pipeline for inferring gender for acknowledged individuals in scientific literature on a massive scale

python nlp analysis hackathon pubmed pubmed-central gender-recognition

Updated Jan 20, 2019
Jupyter Notebook

NCBI-Hackathons / ClusterDuck

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Disease Clustering from Literature Based on Minimal Training Data

snps clustering corpus pubmed literature ncbi

Updated Mar 12, 2020
Python

Coleridge-Initiative / RCApi

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Open

Use "Open Access Journals" category in Wikipedia

ceteri commented Dec 24, 2019

Use "Open Access Journals" category in Wikipedia, to lookup journals. Available via DBpedia.org:

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enhancement good first issue help wanted

Open

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