calcCosine              Calculate the cosine similarity metric for two
                        lists a and b
calcDSEA                Calculate dsea scores of one list in comparison
                        to reference list
calcDice                Calculate the dice similarity metric for two
                        lists a and b
calcEnrichment          Calculate enrichment of one list in comparison
                        to reference list
calcJaccard             Calculate the jaccard coefficient for two lists
                        a and b
cosine                  Calculate cosine similarity metric
createBaseTable         Main function to call everything and produce
                        the results
createDashVectorForATC
                        Creates a vector with an X at each position
                        where a drug from the druglist matches the ATC
                        class list slatc
createJaccardPlotDBMeSH
                        Creates the plot for all jaccard coefficients
                        amongst the three epilepsy ontologies
createJaccardPlotMeSHFive
                        Creates the plot for all jaccard coefficients
                        amongst the three epilepsy ontologies
createNeuroTable        Create the final resulting data frame
createTanimotoBaseline
                        Creates the plot for all jaccard coefficients
                        amongst the three epilepsy ontologies
dice                    Calculate dice similarity metric
doFullPlot              Does the full plot on one page
drawVenn4               Create quad Venn Diagramm for overlapping
                        concepts between EpSO, ESSO, EPILONT and EPISEM
drawVenn4Doc            Create quintuple Venn Diagramm for shared
                        documents with co-occurrences of drug names
                        between EpSO, ESSO, EPILONT and EPISEM
drawVenn4DrugDoc        Create quad Venn Diagramm for shared documents
                        with co-occurrences of drug names between EpSO,
                        ESSO, EPILONT and EPISEM
drawVenn4Syn            Create quad Venn Diagramm for shared synonyms
                        between EpSO, ESSO, EPILONT and EPISEM
drawVenn5               Create quintuple Venn Diagramm for overlapping
                        concepts between EpSO, ESSO, EPILONT, EPISEM
                        and FENICS
drawVenn5Doc            Create quintuple Venn Diagramm for shared
                        documents between EpSO, ESSO, EPILONT, EPISEM
                        and FENICS
drawVenn5DrugDoc        Create quintuple Venn Diagramm for shared
                        documents with co-occurrences of drug names
                        between EpSO, ESSO, EPILONT, EPISEM and FENICS
drawVenn5Syn            Create quintuple Venn Diagramm for shared
                        synonyms between EpSO, ESSO, EPILONT, EPISEM
                        and FENICS
drawVennGrid            Create plot_grid from multiple plots
filterApprovedDrugs     Filter a given list of drug names for having an
                        ATC code, if not they are dropped
filterNeuroDrugs        Filter a given list of drug names for having an
                        ATC code starting with N indicating to be a
                        drug for the Nervous System
genDictListFromRawFreq
                        Clears object that was loaded from harddrive
                        into a list of terms sorted by frequency
getRefAll               Retrieve the list of drugs from the union of
                        all reference lists
getTermMatrix           Receives a sorted hashmap with found entities
                        from a dictionary
jaccard                 Calculate jaccard similarity metric for two
                        sets a and b
plotDSEA                Plotting functions for DSEA lists
plotEnrichment          Plotting functions for enrichment lists
printTop10Drugs         Print Top 10 Drugs
rawDrugNamesCoOcEPILONT
                        List drug terms with their frequency
                        co-occurring with terms from the EPILONT
                        ontology in publications since 2015 from the
                        BioASQ 2020 corpus.
rawDrugNamesCoOcEPISEM
                        List drug terms with their frequency
                        co-occurring with terms from the EPISEM
                        ontology in publications since 2015 from the
                        BioASQ 2020 corpus.
rawDrugNamesCoOcESSO    List drug terms with their frequency
                        co-occurring with terms from the ESSO ontology
                        in publications since 2015 from the BioASQ 2020
                        corpus.
rawDrugNamesCoOcEpSO    List drug terms with their frequency
                        co-occurring with terms from the EpSO ontology
                        in publications since 2015 from the BioASQ 2020
                        corpus.
rawDrugNamesCoOcFENICS
                        List drug terms with their frequency
                        co-occurring with terms from the FENICS
                        ontology in publications from the BioASQ 2020
                        corpus.
readAtcMapIntoHashMapAtcCodesAtcNames
                        Processes the input file db-atc.map to form a
                        HashMap containing the drug names with ATC
                        codes
readAtcMapIntoHashMapDrugNamesAtcCodes
                        Processes the input file db-atc.map to form a
                        HashMap containing the drug names with ATC
                        codes
readSecondLevelATC      Read the second level ATC classes from the file
                        atc-secondlevel.map
sortTableByRefMatches   Sort table by scoring for each row
