CMdictionary            'CMdictionary'
CMdictionary-class      Class that stores a Conceptmapper dictionary
CMoptions               'CMoptions'
CMoptions-class         Class to set the options to run the
                        EntityFinder
CaseMatch               'CaseMatch'
EntityFinder            'EntityFinder'
EntityFinder-class      EntityFinder class to create a Conceptmapper
                        instance
FindAllMatches          Method FindAllMatches
OnASSiS                 OnASSiS (Ontology Annotations and Semantic
                        Similarity software)
Onassis-class           Onassis-class
OrderIndependentLookup
                        'OrderIndependentLookup'
SearchStrategy          Method SearchStrategy
Similarity              'Similarity'
Similarity-class        Similarity class to compute similarities
                        between concepts in ontologies and samples
                        annotated with different concepts
                        'Similarity-class'
Stemmer                 Method Stemmer
StopWords               Method StopWords
SynonymType             Method SynonymType
annotate                'annotate'
annotateDF              'annotateDF'
collapse                'collapse'
compare                 'compare'
connectToGEODB          'connectToGEODB'
dictInfo                Get and Set the dicInfo slot for the
                        'CMdictionary' class
dictRef                 'dictRef'
dictTypes               'dictTypes'
dict_location           'dict_location'
dictionary              'dictionary<-'
entities                'entities<-'
experiment_types        'experiment_types'
filterTerms             'filterTerms'
filterconcepts          'filterconcepts'
findEntities            Method findEntities
findHealthy             'findHealthy'
getGEOMetadata          'getGEOMetadata'
groupConfig             'groupConfig'
groupsim                Method groupsim
groupwiseConfigRef      'groupwiseConfigRef'
icConfig                'icConfig'
listCMOptions           'listCMOptions'
listSimilarities        'listSimilarities'
mergeonassis            'mergeonassis'
multisim                'multisim'
ontology                'ontology<-'
organism_types          'organism_types'
pairsim                 'pairsim'
pairwiseConfig          'pairwiseConfig'
pairwiseConfigRef       'pairwiseConfigRef'
paramValueIndex         Method paramValueIndex
samplesim               'samplesim'
scores                  'scores<-'
sim                     'sim'
simil                   'simil<-'
similarityInstance      'similarityInstance'
typeSystemRef           Method typeSystemRef
