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

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

Introduction to the rif package

rif is an R wrapper for the Neuroscience Information Framework (NIF) APIs.

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

Install

Stable rif version from CRAN

install.packages("rif")

Or, the development version from Github

devtools::install_github("ropensci/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

literature_search(query = "cellular", count = 5)

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

rif documentation built on May 2, 2019, 5:54 a.m.