In ropensci/rif: Client for 'Neuroscience' Information Framework 'APIs'

rif

knitr::opts_chunk$set(
  comment = "#>",
  collapse = FALSE,
  warning = FALSE,
  message = FALSE
)

R client for the Neuroscience Information Framework APIs.

• API docs at https://neuinfo.org/about/webservices

Auth

You now need an API key to use the NIF API. Steps:

• Go to https://www.neuinfo.org/
• If you don't have an account yet, register for an account.
• Log in
• Go to https://www.neuinfo.org/account/developer - you'll need to enter your password again
• Create an API key
• Store your API key ideally as an environment variable in .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.

Installation

CRAN version

install.packages("rif")

development version

install.packages("remotes")
remotes::install_github("ropensci/rif")

Load rif

library('rif')

Summary

out <- rif_summary("cellular")
head(out$result$federationSummary$results)

Query

List NIF query categories

rif_query_categories()

Vocabulary

Search for vocabulary terms

vocabulary_search("cell", limit = 3)

Lexical

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)

Sentences

lexical_sentences(text)

Chunks

head(lexical_chunks(text))

Entities

head(lexical_entities(text))

Literature

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")

Data

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

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rif in R doing citation(package = 'rif')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

ropensci/rif documentation built on May 18, 2022, 6:40 p.m.