COVIDminerAPI is a package to enable easy access from R to the COVIDminer API.
The COVIDminer project is a text mining resource covering the rapidly-expanding literature surrounding the SARS-CoV-2 virus and the COVID-19 pandemic. For more information on this project please visit the COVIDminer website at https://rupertoverall.net/covidminer/ and particularly the tutorial if you are new to the project.
The package can be installed in R using devtools:
devtools::install_github("rupertoverall/COVIDminerAPI", build_vignettes = TRUE)The COVIDminerAPI package is used to construct API queries to the COVIDminer text mining service. Because the functions accept character vectors and return data frames and lists, this package makes calling the web service and parsing the response fit seamlessly into your R code.
A example session is shown below:
# The api_search function is used to retrieve COVIDminer identifiers for two entities.
search.response = COVIDminerAPI::api_search(query = c("bdnf", "autophagy"))
# The most useful field in the results is 'best-match', which returns a single identifier for each query term.
best.matches = search.response$results$`best-match`
# The best matching identifiers can then be passed to the api_get function to get the interaction network.
get.response = COVIDminerAPI::api_get(query = best.matches, filters = "default")
# If you want to use network analysis tools, then a simple edge list is a good starting point.
edge.list = get.response$results[, c("source", "relation", "target")]