EntityFinder: 'EntityFinder'
In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description Usage Arguments Value Examples

this function creates instances of the class EntityFinder

1 2	EntityFinder(input, dictionary, options = NA, outDir = tempdir(), multipleDocs = FALSE)

`input`	the file, directory, or data frame with the text to annotate
`dictionary`	A dictionary of the type `CMdictionary` or the path to an already created Conceptmapper XML file
`options`	an object of class `CMoptions`. If NA, the default configuration will be set.
`outDir`	the directory where the annotated files will be stored
`multipleDocs`	TRUE when multiple documents are loaded from a single file with each row representing a document. The file should have two columns. The first for the unique document identifier and the second for the textual descriptions

dataframe of annotations

obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
sample_dict <- CMdictionary(input=obo, outputDir=getwd(), synonymType='ALL')
myopts <- CMoptions()
paramValueIndex(myopts) <- 40
entities <- EntityFinder(input=readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds', package='Onassis')), dictionary=sample_dict, options=myopts)