knitr::opts_chunk$set( comment = "#>", collapse = FALSE, warning = FALSE, message = FALSE )
R client for the Neuroscience Information Framework APIs.
You now need an API key to use the NIF API. Steps:
.Renviron
or similar. Or, you can save as an R option. (see ?Startup
for help on
env vars and R options). You can also pass in your API key to each function
but that's not ideal.CRAN version
install.packages("rif")
development version
install.packages("remotes") remotes::install_github("ropensci/rif")
Load rif
library('rif')
out <- rif_summary("cellular") head(out$result$federationSummary$results)
List NIF query categories
rif_query_categories()
Search for vocabulary terms
vocabulary_search("cell", limit = 3)
Break up text into various things
text <- "Lorem ipsum inceptos dolor nisi torquent porttitor donec, blandit scelerisque mattis cras quis mi, aliquam sagittis. Convallis placerat commodo imperdiet varius nunc tempus urna vitae ultrices tristique eu mi ornare velit donec, posuere laoreet pretium vitae porta augue porta feugiat in sapien egestas. Quam odio nullam pulvinar litora curabitur amet lacus sociosqu gravida ligula molestie dui netus fusce bibendum scelerisque, dictum malesuada proin elit etiam aliquam, mattis euismod donec nisl facilisis." text <- gsub("\n", "", text)
lexical_sentences(text)
head(lexical_chunks(text))
head(lexical_entities(text))
Search
library("dplyr") out <- literature_search(query = "cellular", count = 5) out$result$publications %>% select(pmid, journal, year)
Get retractions
out <- literature_retractions() out[1:20]
Then get info on some articles
arts <- literature_pmid(pmid = out[1:2]) lapply(arts, "[[", "title")
Search for data
out <- federation_search("cellular") out$query head(out$result$results)
Get some data
out <- federation_data(id = "nlx_152871-2") out$result$result
rif
in R doing citation(package = 'rif')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.