## ----echo=TRUE, eval=TRUE----------------------------------------------------- require(rJava) #Initializing the JVM .jinit() #Adding the path to the jar file jarfilePath <- file.path(system.file('extdata', 'java', 'conceptmapper-0.0.1-SNAPSHOT-jar-with-dependencies.jar', package='OnassisJavaLibs')) .jaddClassPath(jarfilePath) #Creating an instance of the OntologyUtil with the sample obo file ontoutil <- .jnew("edu.ucdenver.ccp.datasource.fileparsers.obo.OntologyUtil", .jnew('java/io/File', file.path(system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')))) #Creating the output file containing the conceptmapper dictionary outputFile = .jnew("java/io/File", "dict.xml") #Building of the dictionary from the OBO ontology dictionary <- J("edu.ucdenver.ccp.nlp.wrapper.conceptmapper.dictionary.obo.OboToDictionary")$buildDictionary( outputFile, ontoutil, .jnull(), J("edu.ucdenver.ccp.datasource.fileparsers.obo.OntologyUtil")$SynonymType$EXACT ) ## ----echo=TRUE, eval=TRUE----------------------------------------------------- #Adding the similarity library containing the similarity class to compute semantic similarities jarfilePath <- file.path(system.file('extdata', 'java', 'similarity-0.0.1-SNAPSHOT-jar-with-dependencies.jar', package='OnassisJavaLibs')) .jaddClassPath(jarfilePath) #Creating an instance of the class Similarity similarity <- .jnew("iit/comp/epigen/nlp/similarity/Similarity") #Loading the ontology in a grah structure file_obo <- file.path(system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')) ontology_graph <- similarity$loadOntology(file_obo) #Setting the semantic similarity measures measure_configuration <- similarity$setPairwiseConfig('resnik', 'seco') #Terms of the ontologies need to be converted into URIs term1 <- 'http://purl.obolibrary.org/obo/CL_0000771' term2 <- 'http://purl.obolibrary.org/obo/CL_0000988' URI1 <- .jcast(similarity$createURI(term1), new.class = "org.openrdf.model.URI", check = FALSE, convert.array = FALSE) URI2 <- .jcast(similarity$createURI(term2), new.class = "org.openrdf.model.URI", check = FALSE, convert.array = FALSE) # Computation of the semantic similarity score similarity_score <- .jcall(similarity, "D", "pair_similarity", URI1, URI2, .jcast(ontology_graph, new.class = "slib.graph.model.graph.G"), measure_configuration) similarity_score