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  "Package": "epos",
  "Type": "Package",
  "Title": "Epilepsy Ontologies' Similarities",
  "Version": "1.2",
  "Maintainer": "Bernd Mueller <bernd.mueller@zbmed.de>",
  "Description": "Analysis and visualization of similarities between\nepilepsy ontologies based on text mining results by comparing\nranked lists of co-occurring drug terms in the BioASQ corpus.\nThe ranked result lists of neurological drug terms co-occurring\nwith terms from the epilepsy ontologies EpSO, ESSO, EPILONT,\nEPISEM and FENICS undergo further analysis. The source data to\ncreate the ranked lists of drug names is produced using the\ntext mining workflows described in Mueller, Bernd and\nHagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>,\nMueller, Bernd et al. (2017)\n<doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and\nRebholz-Schuhmann, Dietrich (2020)\n<doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al.\n(2022) <doi:10.1186/s13326-021-00258-w>.",
  "License": "LGPL (>= 3)",
  "Encoding": "UTF-8",
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  "URL": "https://github.com/bernd-mueller/epos",
  "BugReports": "https://github.com/bernd-mueller/epos/issues",
  "Authors@R": "person(given = \"Bernd\",\nfamily = \"Mueller\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3062-8192\"),\nemail = \"bernd.mueller@zbmed.de\")",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibsasl2-dev",
  "Repository": "https://bernd-mueller.r-universe.dev",
  "Date/Publication": "2025-08-29 11:33:43 UTC",
  "RemoteUrl": "https://github.com/bernd-mueller/epos",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 07:59:16 UTC",
    "User": "root"
  },
  "Author": "Bernd Mueller [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3062-8192>)",
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  "_published": "2026-05-26T08:05:29.484Z",
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      "package": "VennDiagram",
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  "_realowner": "bernd-mueller",
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      "date": "2018-10-08"
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      "date": "2021-02-20"
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      "date": "2024-03-15"
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  "_exports": [
    "calcCosine",
    "calcDice",
    "calcDSEA",
    "calcEnrichment",
    "calcJaccard",
    "cosine",
    "createBaseTable",
    "createDashVectorForATC",
    "createNeuroTable",
    "createTanimotoBaseline",
    "dice",
    "drawVenn4",
    "drawVenn4Doc",
    "drawVenn4DrugDoc",
    "drawVenn4Syn",
    "drawVenn5",
    "drawVenn5Doc",
    "drawVenn5DrugDoc",
    "drawVenn5Syn",
    "drawVennGrid",
    "filterApprovedDrugs",
    "filterNeuroDrugs",
    "genDictListFromRawFreq",
    "getRefAll",
    "getTermMatrix",
    "jaccard",
    "plotDSEA",
    "plotEnrichment",
    "printTop10Drugs",
    "readAtcMapIntoHashMapAtcCodesAtcNames",
    "readAtcMapIntoHashMapDrugNamesAtcCodes",
    "readSecondLevelATC",
    "sortTableByRefMatches"
  ],
  "_datasets": [
    {
      "name": "rawDrugNamesCoOcEPILONT",
      "title": "List drug terms with their frequency co-occurring with terms from the EPILONT ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "object": "rawDrugNamesCoOcEPILONT",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rawDrugNamesCoOcEPISEM",
      "title": "List drug terms with their frequency co-occurring with terms from the EPISEM ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "object": "rawDrugNamesCoOcEPISEM",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rawDrugNamesCoOcEpSO",
      "title": "List drug terms with their frequency co-occurring with terms from the EpSO ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "object": "rawDrugNamesCoOcEpSO",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rawDrugNamesCoOcESSO",
      "title": "List drug terms with their frequency co-occurring with terms from the ESSO ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "object": "rawDrugNamesCoOcESSO",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rawDrugNamesCoOcFENICS",
      "title": "List drug terms with their frequency co-occurring with terms from the FENICS ontology in publications from the BioASQ 2020 corpus.",
      "object": "rawDrugNamesCoOcFENICS",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calcCosine",
      "title": "Calculate the cosine similarity metric for two lists a and b",
      "topics": [
        "calcCosine"
      ]
    },
    {
      "page": "calcDice",
      "title": "Calculate the dice similarity metric for two lists a and b",
      "topics": [
        "calcDice"
      ]
    },
    {
      "page": "calcDSEA",
      "title": "Calculate dsea scores of one list in comparison to reference list",
      "topics": [
        "calcDSEA"
      ]
    },
    {
      "page": "calcEnrichment",
      "title": "Calculate enrichment of one list in comparison to reference list",
      "topics": [
        "calcEnrichment"
      ]
    },
    {
      "page": "calcJaccard",
      "title": "Calculate the jaccard coefficient for two lists a and b",
      "topics": [
        "calcJaccard"
      ]
    },
    {
      "page": "cosine",
      "title": "Calculate cosine similarity metric",
      "topics": [
        "cosine"
      ]
    },
    {
      "page": "createBaseTable",
      "title": "Main function to call everything and produce the results",
      "topics": [
        "createBaseTable"
      ]
    },
    {
      "page": "createDashVectorForATC",
      "title": "Creates a vector with an X at each position where a drug from the druglist matches the ATC class list slatc",
      "topics": [
        "createDashVectorForATC"
      ]
    },
    {
      "page": "createJaccardPlotDBMeSH",
      "title": "Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies",
      "topics": [
        "createJaccardPlotDBMeSH"
      ]
    },
    {
      "page": "createJaccardPlotMeSHFive",
      "title": "Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies",
      "topics": [
        "createJaccardPlotMeSHFive"
      ]
    },
    {
      "page": "createNeuroTable",
      "title": "Create the final resulting data frame",
      "topics": [
        "createNeuroTable"
      ]
    },
    {
      "page": "createTanimotoBaseline",
      "title": "Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies",
      "topics": [
        "createTanimotoBaseline"
      ]
    },
    {
      "page": "dice",
      "title": "Calculate dice similarity metric",
      "topics": [
        "dice"
      ]
    },
    {
      "page": "doFullPlot",
      "title": "Does the full plot on one page",
      "topics": [
        "doFullPlot"
      ]
    },
    {
      "page": "drawVenn4",
      "title": "Create quad Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT and EPISEM",
      "topics": [
        "drawVenn4"
      ]
    },
    {
      "page": "drawVenn4Doc",
      "title": "Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEM",
      "topics": [
        "drawVenn4Doc"
      ]
    },
    {
      "page": "drawVenn4DrugDoc",
      "title": "Create quad Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEM",
      "topics": [
        "drawVenn4DrugDoc"
      ]
    },
    {
      "page": "drawVenn4Syn",
      "title": "Create quad Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT and EPISEM",
      "topics": [
        "drawVenn4Syn"
      ]
    },
    {
      "page": "drawVenn5",
      "title": "Create quintuple Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT, EPISEM and FENICS",
      "topics": [
        "drawVenn5"
      ]
    },
    {
      "page": "drawVenn5Doc",
      "title": "Create quintuple Venn Diagramm for shared documents between EpSO, ESSO, EPILONT, EPISEM and FENICS",
      "topics": [
        "drawVenn5Doc"
      ]
    },
    {
      "page": "drawVenn5DrugDoc",
      "title": "Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT, EPISEM and FENICS",
      "topics": [
        "drawVenn5DrugDoc"
      ]
    },
    {
      "page": "drawVenn5Syn",
      "title": "Create quintuple Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT, EPISEM and FENICS",
      "topics": [
        "drawVenn5Syn"
      ]
    },
    {
      "page": "drawVennGrid",
      "title": "Create plot_grid from multiple plots",
      "topics": [
        "drawVennGrid"
      ]
    },
    {
      "page": "filterApprovedDrugs",
      "title": "Filter a given list of drug names for having an ATC code, if not they are dropped",
      "topics": [
        "filterApprovedDrugs"
      ]
    },
    {
      "page": "filterNeuroDrugs",
      "title": "Filter a given list of drug names for having an ATC code starting with N indicating to be a drug for the Nervous System",
      "topics": [
        "filterNeuroDrugs"
      ]
    },
    {
      "page": "genDictListFromRawFreq",
      "title": "Clears object that was loaded from harddrive into a list of terms sorted by frequency",
      "topics": [
        "genDictListFromRawFreq"
      ]
    },
    {
      "page": "getRefAll",
      "title": "Retrieve the list of drugs from the union of all reference lists",
      "topics": [
        "getRefAll"
      ]
    },
    {
      "page": "getTermMatrix",
      "title": "Receives a sorted hashmap with found entities from a dictionary",
      "topics": [
        "getTermMatrix"
      ]
    },
    {
      "page": "jaccard",
      "title": "Calculate jaccard similarity metric for two sets a and b",
      "topics": [
        "jaccard"
      ]
    },
    {
      "page": "plotDSEA",
      "title": "Plotting functions for DSEA lists",
      "topics": [
        "plotDSEA"
      ]
    },
    {
      "page": "plotEnrichment",
      "title": "Plotting functions for enrichment lists",
      "topics": [
        "plotEnrichment"
      ]
    },
    {
      "page": "printTop10Drugs",
      "title": "Print Top 10 Drugs",
      "topics": [
        "printTop10Drugs"
      ]
    },
    {
      "page": "rawDrugNamesCoOcEPILONT",
      "title": "List drug terms with their frequency co-occurring with terms from the EPILONT ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "topics": [
        "rawDrugNamesCoOcEPILONT"
      ]
    },
    {
      "page": "rawDrugNamesCoOcEPISEM",
      "title": "List drug terms with their frequency co-occurring with terms from the EPISEM ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "topics": [
        "rawDrugNamesCoOcEPISEM"
      ]
    },
    {
      "page": "rawDrugNamesCoOcEpSO",
      "title": "List drug terms with their frequency co-occurring with terms from the EpSO ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "topics": [
        "rawDrugNamesCoOcEpSO"
      ]
    },
    {
      "page": "rawDrugNamesCoOcESSO",
      "title": "List drug terms with their frequency co-occurring with terms from the ESSO ontology in publications since 2015 from the BioASQ 2020 corpus.",
      "topics": [
        "rawDrugNamesCoOcESSO"
      ]
    },
    {
      "page": "rawDrugNamesCoOcFENICS",
      "title": "List drug terms with their frequency co-occurring with terms from the FENICS ontology in publications from the BioASQ 2020 corpus.",
      "topics": [
        "rawDrugNamesCoOcFENICS"
      ]
    },
    {
      "page": "readAtcMapIntoHashMapAtcCodesAtcNames",
      "title": "Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codes",
      "topics": [
        "readAtcMapIntoHashMapAtcCodesAtcNames"
      ]
    },
    {
      "page": "readAtcMapIntoHashMapDrugNamesAtcCodes",
      "title": "Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codes",
      "topics": [
        "readAtcMapIntoHashMapDrugNamesAtcCodes"
      ]
    },
    {
      "page": "readSecondLevelATC",
      "title": "Read the second level ATC classes from the file atc-secondlevel.map",
      "topics": [
        "readSecondLevelATC"
      ]
    },
    {
      "page": "sortTableByRefMatches",
      "title": "Sort table by scoring for each row",
      "topics": [
        "sortTableByRefMatches"
      ]
    }
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