Package: epos 1.1

epos: Epilepsy Ontologies' Similarities

Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.

Authors:Bernd Mueller

epos_1.1.tar.gz
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epos.pdf |epos.html✨
epos/json (API)

# Install 'epos' in R:
install.packages('epos', repos = c('https://bernd-mueller.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bernd-mueller/epos/issues

Datasets:
  • 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.

On CRAN:

33 exports 1.76 score 97 dependencies 4 mentions 53 scripts 247 downloads

Last updated 6 months agofrom:2fc4cc21b1. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 11 2024
R-4.5-winNOTESep 11 2024
R-4.5-linuxNOTESep 11 2024
R-4.4-winNOTESep 11 2024
R-4.4-macNOTESep 11 2024
R-4.3-winNOTESep 11 2024
R-4.3-macNOTESep 11 2024

Exports:calcCosinecalcDicecalcDSEAcalcEnrichmentcalcJaccardcosinecreateBaseTablecreateDashVectorForATCcreateNeuroTablecreateTanimotoBaselinedicedrawVenn4drawVenn4DocdrawVenn4DrugDocdrawVenn4SyndrawVenn5drawVenn5DocdrawVenn5DrugDocdrawVenn5SyndrawVennGridfilterApprovedDrugsfilterNeuroDrugsgenDictListFromRawFreqgetRefAllgetTermMatrixjaccardplotDSEAplotEnrichmentprintTop10DrugsreadAtcMapIntoHashMapAtcCodesAtcNamesreadAtcMapIntoHashMapDrugNamesAtcCodesreadSecondLevelATCsortTableByRefMatches

Dependencies:askpassbackportsbase64encbitopsbriobslibcachemcallrcaToolscheckmatecliclustercolorspacecowplotcrayondata.tabledescdiffobjdigestevaluatefansifarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsggplot2gluegplotsgridExtragtablegtoolshashhighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemongolitemunsellnlmennetopensslpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6rappdirsRColorBrewerrematch2rlangrmarkdownrpartrprojrootrstudioapisassscalesstringistringrsystestthattibbletinytexTopKListsutf8vctrsVennDiagramviridisviridisLitewaldowithrxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
Calculate the cosine similarity metric for two lists a and bcalcCosine
Calculate the dice similarity metric for two lists a and bcalcDice
Calculate dsea scores of one list in comparison to reference listcalcDSEA
Calculate enrichment of one list in comparison to reference listcalcEnrichment
Calculate the jaccard coefficient for two lists a and bcalcJaccard
Calculate cosine similarity metriccosine
Main function to call everything and produce the resultscreateBaseTable
Creates a vector with an X at each position where a drug from the druglist matches the ATC class list slatccreateDashVectorForATC
Creates the plot for all jaccard coefficients amongst the three epilepsy ontologiescreateJaccardPlotDBMeSH
Creates the plot for all jaccard coefficients amongst the three epilepsy ontologiescreateJaccardPlotMeSHFive
Create the final resulting data framecreateNeuroTable
Creates the plot for all jaccard coefficients amongst the three epilepsy ontologiescreateTanimotoBaseline
Calculate dice similarity metricdice
Does the full plot on one pagedoFullPlot
Create quad Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT and EPISEMdrawVenn4
Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEMdrawVenn4Doc
Create quad Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEMdrawVenn4DrugDoc
Create quad Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT and EPISEMdrawVenn4Syn
Create quintuple Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT, EPISEM and FENICSdrawVenn5
Create quintuple Venn Diagramm for shared documents between EpSO, ESSO, EPILONT, EPISEM and FENICSdrawVenn5Doc
Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT, EPISEM and FENICSdrawVenn5DrugDoc
Create quintuple Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT, EPISEM and FENICSdrawVenn5Syn
Create plot_grid from multiple plotsdrawVennGrid
Filter a given list of drug names for having an ATC code, if not they are droppedfilterApprovedDrugs
Filter a given list of drug names for having an ATC code starting with N indicating to be a drug for the Nervous SystemfilterNeuroDrugs
Clears object that was loaded from harddrive into a list of terms sorted by frequencygenDictListFromRawFreq
Retrieve the list of drugs from the union of all reference listsgetRefAll
Receives a sorted hashmap with found entities from a dictionarygetTermMatrix
Calculate jaccard similarity metric for two sets a and bjaccard
Plotting functions for DSEA listsplotDSEA
Plotting functions for enrichment listsplotEnrichment
Print Top 10 DrugsprintTop10Drugs
List drug terms with their frequency co-occurring with terms from the EPILONT ontology in publications since 2015 from the BioASQ 2020 corpus.rawDrugNamesCoOcEPILONT
List drug terms with their frequency co-occurring with terms from the EPISEM ontology in publications since 2015 from the BioASQ 2020 corpus.rawDrugNamesCoOcEPISEM
List drug terms with their frequency co-occurring with terms from the EpSO ontology in publications since 2015 from the BioASQ 2020 corpus.rawDrugNamesCoOcEpSO
List drug terms with their frequency co-occurring with terms from the ESSO ontology in publications since 2015 from the BioASQ 2020 corpus.rawDrugNamesCoOcESSO
List drug terms with their frequency co-occurring with terms from the FENICS ontology in publications from the BioASQ 2020 corpus.rawDrugNamesCoOcFENICS
Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codesreadAtcMapIntoHashMapAtcCodesAtcNames
Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codesreadAtcMapIntoHashMapDrugNamesAtcCodes
Read the second level ATC classes from the file atc-secondlevel.mapreadSecondLevelATC
Sort table by scoring for each rowsortTableByRefMatches