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'
annotateTissueDisease   'annotateTissueDisease'
collapse                'collapse'
compare                 'compare'
connectToGEODB          'connectToGEODB'
create_score_matrix     'createScoreMatrix'
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<-'
semanticdifference      'semanticdifference'
sim                     'sim'
simil                   'simil<-'
similarityInstance      'similarityInstance'
typeSystemRef           Method typeSystemRef
