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This package enables license holders to access SciBite API functionality using R
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Project Description

R package for making calls to SciBite's NER engine, TERMite, as well as the TExpress module for defining more complex semantic patterns.


  1. First you will need to install and load the devtools package
  1. You can then install the package directly from their GitHub repository
install_github('SciBiteLabs/R_toolkit', subdir = 'SciBiteR')

Basic usage

First you need to load the package


You can then make a call to the TERMite API. Here we send some example text and get a JSON response.

endpoint <- "http://localhost:9090/termite"
input <- "PAXIP1 Potentiates the Combination of WEE1 Inhibitor AZD1775 and Platinum Agents in Lung Cancer. The DNA damage response (DDR) involves a complex network of signaling events mediated by modular protein domains such as the BRCA1 C-terminal (BRCT) domain."
inputFile <- FALSE
inputFileFormat <- NULL
outputFile <- NULL
outputFormat <- "json"
VOCabs <- NULL
options <- list("subsume" = "false", "rejectAmbig" = "true")

termiteResponse <- TERMite(endpoint="http://localhost:9090/termite",
        input = input,
        inputFile = inputFile,
        inputFileFormat = inputFileFormat,
        outputFile = outputFile,
        outputFormat = outputFormat,
        VOCabs = VOCabs,
        options = options)

The JSON response can then be converted into a more useable dataframe

responseDF <- get_entity_hits_from_json(termiteResponse)

Other examples of using the R toolkit can be found in the example scripts

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