In frequena/bioloupe: Interface with APIs related to biomedical Named-Entity recognition (NER) using R

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

bioloupe

Installation

You can install the development version from Github.

# install.packages("devtools")
devtools::install_github("frequena/bioloupe")

Overview

The package bioloupe provides an interface to:

• PubTator API
• Biolink API

Examples

Find biomedical entities of PubMed titles and abstracts

library(bioloupe)

b <- find_pubtator(pmid = c(23819905, 23819906, 32220312), bioconcept = 'gene')

b[[2]]$dataframe

...or retrieve the result as HTML code:

b[[2]]$abstract_tagged

Find biomedical entities from a text

Using SciGraph

abstract_input <- 'Marfan syndrome is a multisystemic genetic condition affecting connective tissue. It carries a reduced life expectancy, largely dependent on cardiovascular complications. More common cardiac manifestations such as aortic dissection and aortic valve incompetence have been widely documented in the literature. Mitral valve prolapse (MVP), however, has remained poorly documented. This article aims at exploring the existing literature on the pathophysiology and diagnosis of MVP in patients with Marfan syndrome, defining its current management and outlining the future developments surrounding it.'

result <- find_scigraph(text = abstract_input) 
result$content

frequena/bioloupe documentation built on March 3, 2021, 12:32 a.m.