# Epilepsy Ontologies' Similarities

## Documentation for package ‘epos’ version 1.0

- DESCRIPTION file.

## Help Pages

calcCosine | Calculate the cosine similarity metric for two lists a and b
calcDice | Calculate the dice similarity metric for two lists a and b
calcDSEA | Calculate dsea scores of one list in comparison to reference list
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.
rawDrugNamesCoOcEpSO | List drug terms with their frequency co-occurring with terms from the EpSO 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.
rawDrugNamesCoOcFENICS | List drug terms with their frequency co-occurring with terms from the FENICS ontology in publications since 2015 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