pairsim: 'pairsim'

In eugeniaeueu/Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method computes the semantic similarity between two terms of a given ontology.

Usage

pairsim(object, term1, term2)

## S4 method for signature 'Similarity,character,character'
pairsim(object, term1, term2)

Arguments

object	instance of class Similarity-class
term1	The URI of the ontology term in the format http://purl.obolibrary.org/obo/Ontology_id (e.g 'http://purl.obolibrary.org/obo/CL_0000542')
term2	The URI of the ontology term

Value

the semantic similarity of the two provided concepts

Examples

sim <- new('Similarity')
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
ontology(sim) <- obo
pairwiseConfig(sim) <- listSimilarities()$pairwiseMeasures[9]
similarity <- pairsim(sim, 'http://purl.obolibrary.org/obo/CL_0000542',
'http://purl.obolibrary.org/obo/CL_0000236')

eugeniaeueu/Onassis documentation built on March 9, 2020, 8:17 a.m.