R/Lexicons.R

In ropensci/EndoMineR: Functions to mine endoscopic and associated pathology datasets

########## Lexicons ##########

#' Use list of pathology types
#'
#' This standardizes terms to describe the pathology tissue type being examined
#' @keywords Pathology type
#' @family NLP - Lexicons
#' @export

HistolType <- function() {

  # First standardise the terms

  tissue <- list(
    "Resection" = "Resection",
    "bx|biopsies" = "Biopsy",
    "(endoscopic mucosal resection)|(endoscopic mucosectomy)" = "EMR",
    "endoscopic submucosal (dissection|resection)" = "ESD",
    "nodul" = "nodul",
    "polyp" = "polyp",
    "emr" = "EMR"
  )


  # To get the list as a list of values only in a regex use
  # paste0(unlist(HistolType(),use.names=F),collapse="|")

  return(tissue)
}



#' Use list of upper and lower GI standard locations
#'

#' The is a list of standard locations at endoscopy. It used for the site of biopsies/EMRs 
#' and potentially in functions looking at the site of a 
#' therapeutic event. It just returns the list in the function.

#'
#'
#' @keywords Location
#' @family NLP - Lexicons
#' @export

LocationList <- function() {
  All <- append(LocationListLower(), LocationListUpper())
  All <- append(All, LocationListUniversal())

  # To get the list as a list of values only in a regex use
  # paste0(unlist(All,use.names=F),collapse="|")

  return(All)
}

#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the
#' extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a 
#' therapeutic event. It just returns the list in the function.

#'
#'
#' @keywords Location
#' @family NLP - Lexicons
#' @export

LocationListUpper <- function() {
  upper <- list(
    "duodenum|d2|D2|duodenal" = "Duodenum",
    "gastric|stomach" = "Stomach",
    "antrum|antral" = "Antrum",
    "ogj|goj|gastrooesophageal" = "GOJ",
    "fundal|fundus" = "stomach",
    "pyloric" = "Pylorus",
    "gastric cardia" = "Cardia",
    "oesophagus|oesophageal" = "Oesophagus"
  )


  # To get the list as a list of values only in a regex use
  # paste0(unlist(upper,use.names=F),collapse="|")

  return(upper)
}

#' Use list of standard locations for upper GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the
#' extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @family NLP - Lexicons
#' @export

LocationListUniversal <- function() {
  universal <- list("Anastomosis" = "Ascending ")
  return(universal)

  # If need to use then use
  # paste0(unlist(universal,use.names=F),collapse="|")
}


#' Use list of standard locations for lower GI endoscopy
#'
#' The is a list of standard locations at endoscopy that is used in the
#' extraction of the site of biopsies/EMRs and potentially in functions looking at the site of a
#' therapeutic event. It just returns the list in the function
#'
#'
#' @keywords Location
#' @family NLP - Lexicons
#' @export

LocationListLower <- function() {
  lower <- list(
    "asce |ascending|(ascend[^a-z])|( colon r )|(r colon)|(asc )|(right colon)" = "Ascending ",
    "descending|(descen[^a-z])|(desc[^a-z])|(des[^a-z])|(colon l)|(l colon)|(left colon)" = "Descending ",
    "sigmoid|(sigm[^a-z])|sigmo " = "Sigmoid ",
    "rectal|rectum|(rectum[a-z])|rect " = "Rectum ",
    "transverse|(transv[^a-z])|tranv |trans " = "Transverse ",
    "caecum|caecal" = "Caecum ",
    "splenic" = "Splenic ",
    "(ileum )|( ileal )" = "Ileum ",
    "rectosigmoid" = "Rectosigmoid ",
    "(ileocaecal\\s*)|icv|(ileo-caecum)" = "Ileocaecal",
    "(hep[^a-z])|([Hh]epatic)" = "Hepatic ",
    "colonic|colon |(col[^a-z])" = "Colon ",
    "term |terminal" = "Terminal",
    "TI " = "Terminal",
    "caec" = "Caecum ",
    "[Ss]ig " = "Sigmoid ",
    "ileo\\s*-\\s*anal|ileo\\s*anal " = "Ileoanal ",
    "(pre\\s*pouch)|(pre-[Pp]ouch)" = "PrePouch",
    "pouch" = "Pouch",
    "term |terminal" = "Terminal"
  )


  # To get the list as a list of values only in a regex use
  # paste0(unlist(lower,use.names=F),collapse="|")

  return(lower)
}


#' Use list of catheters used in radiofrequency ablation
#'
#' The takes a list of catheters used in radiofrequency ablation.
#'
#' @keywords RFA
#' @family NLP - Lexicons
#' @export

RFACath <- function() {
  tofind <-
    paste(
      c(
        "90", "360", "HALO60", " 60", "TTS",
        "[Cc]hannel", "APC"
      ),
      collapse = "|"
    )

  return(tofind)
}

#' Use list of endoscopic events and procedures
#'

#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardisation function
#' This does not include EMR as this is

#' extracted from the pathology so is part of pathology type.
#' @keywords Event extraction
#' @family NLP - Lexicons
#' @examples
#' # unique(unlist(EventList(), use.names = FALSE))
#' @export

EventList <- function() {
  Event <- list(
    "radiofrequency ablation" = "RFA",
    "(argon plasma coagulation)|apc" = "APC",
    "halo| rfa" = "RFA",
    "dilatation|dilated" = "dilat",
    "clip" = "clip",
    "grasp" = "grasp",
    "iodine" = "iodine",
    "acetic" = "acetic",
    "NAC" = "NAC",
    "Brushings" = "brushings",
    " cryo" = "cryablation"
  )

  # To get the list as a list of values only in a regex use
  # paste0(unlist(Event,use.names=F),collapse="|")

  return(Event)
}


#' Index biopsy locations
#'
#' This function returns all the conversions from common version of events to
#' a standardised event list, much like the Location standardidastion function
#' This does not include EMR as this is 
#' extracted from the pathology so is part of pathology type. It is used for
#' automated OPCS-4 coding.
#' @keywords Event extraction
#' @family NLP - Lexicons
#' @export

BiopsyIndex <- function() {
  BiopsyIndexList <- list(
    "ileum:biopsy" = "C11",
    "ileocaecal:biopsy" = "C10",
    "caecum:biopsy" = "C9",
    "ascending:biopsy" = "C8",
    "hepatic:biopsy" = "C7",
    "transverse:biopsy" = "C6",
    "splenic:biopsy" = "C5",
    "descending:biopsy" = "C4",
    "sigmoid:biopsy" = "C3",
    "rectosigmoid:biopsy" = "C2",
    "rectum:biopsy" = "C1",
    "ileoanal:biopsy" = "S1",
    "prepouch:biopsy" = "S2",
    "pouch:biopsy" = "S3",
    "duodenum:biopsy" = "O5",
    "antrum:biopsy" = "O4",
    "stomach:biopsy" = "O3",
    "goj:biopsy" = "O1",
    "cardia:biopsy" = "O2",
    "oesophagus:biopsy" = "O1",
    "colon:biopsy" = "colon",
    "oesophagus:emr" = "O1",
    "goj:emr" = "O1",
    "stomach:emr" = "O3",
    "duodenum:emr" = "O5"
  )

  # To get the list as a list of values only in a regex use
  # paste0(unlist(BiopsyIndex,use.names=F),collapse="|")

  return(BiopsyIndexList)
}



#' Index of GI symptoms
#'
#' This function returns all the common GI symptoms. 
#' They are simply listed as is without grouping
#' or mapping. They have been derived from a manual 
#' list with synonyms derived from the UMLS Methatharus
#' using the browser.
#' @keywords Event extraction
#' @family NLP - Lexicons
#' @export

GISymptomsList <- function() {
  Symptoms <- list(
    "abdomen pain" = "abdomen pain",
    "abdomen; pain, epigastric" = "abdomen; pain, epigastric",
    "abdominal pain" = "abdominal pain",
    "abdominal pain epigastric" = "abdominal pain epigastric",
    "abdominal pain in the central upper belly" = "abdominal pain in the central upper belly",
    "abdominal pain nos" = "abdominal pain nos",
    "abdominal pain, epigastric" = "abdominal pain, epigastric",
    "abdominal pain, unspecified site" = "abdominal pain, unspecified site",
    "abdominal pains" = "abdominal pains",
    "abdominal wind" = "abdominal wind",
    "abdominal; pain" = "abdominal; pain",
    "abdominalgia" = "abdominalgia",
    "acid reflux" = "acid reflux",
    "acidity" = "acidity",
    "alteration in bowel elimination: incontinence" = "alteration in bowel elimination: incontinence",
    "altered blood in stool" = "altered blood in stool",
    "altered blood passed per rectum" = "altered blood passed per rectum",
    "anal incontinence" = "anal incontinence",
    "anal pain" = "anal pain",
    "anus pain" = "anus pain",
    "anus pains" = "anus pains",
    "anus; pain" = "anus; pain",
    "ap - abdominal pain" = "ap - abdominal pain",
    "bad breath" = "bad breath",
    "bad breath - halitosis" = "bad breath - halitosis",
    "bad breath halitosis" = "bad breath halitosis",
    "bad or foul breath" = "bad or foul breath",
    "bad/foul;breath" = "bad/foul;breath",
    "being sick" = "being sick",
    "belch" = "belch",
    "belching" = "belching",
    "belching symptom" = "belching symptom",
    "belching symptoms" = "belching symptoms",
    "belching, burping" = "belching, burping",
    "belchings" = "belchings",
    "bellyache" = "bellyache",
    "black stool" = "black stool",
    "black stools" = "black stools",
    "black, tarry stool" = "black, tarry stool",
    "bleeding per rectum" = "bleeding per rectum",
    "bleeding rectal" = "bleeding rectal",
    "bleeding rectum" = "bleeding rectum",
    "bleeding-rectal" = "bleeding-rectal",
    "bleeding;anal" = "bleeding;anal",
    "bleeding;rectal" = "bleeding;rectal",
    "blood per rectum" = "blood per rectum",
    "blood; vomiting" = "blood; vomiting",
    "bowel incontinena" = "bowel incontinena",
    "bowel incontinence" = "bowel incontinence",
    "bowel incontinent" = "bowel incontinent",
    "bowel loose movements" = "bowel loose movements",
    "bowels loose movement" = "bowels loose movement",
    "bowels: incontinent" = "bowels: incontinent",
    "brash" = "brash",
    "breath odor" = "breath odor",
    "breath odor abnormal" = "breath odor abnormal",
    "breath odor nos" = "breath odor nos",
    "breath odors" = "breath odors",
    "breath odour" = "breath odour",
    "breath odour nos" = "breath odour nos",
    "breath smells offensive" = "breath smells offensive",
    "breath smells unpleasant" = "breath smells unpleasant",
    "breath; foul" = "breath; foul",
    "burning reflux" = "burning reflux",
    "burp" = "burp",
    "burping" = "burping",
    "burps" = "burps",
    "c/o - cough" = "c/o - cough",
    "can't get food down" = "can't get food down",
    "cannot get food down" = "cannot get food down",
    "chest pain" = "chest pain",
    "chest pain nos" = "chest pain nos",
    "chest pain or discomfort" = "chest pain or discomfort",
    "chest pain or discomfort reported as pain" = "chest pain or discomfort reported as pain",
    "chest pain, nos" = "chest pain, nos",
    "chest pain, pleuritic" = "chest pain, pleuritic",
    "chest pain, unspecified" = "chest pain, unspecified",
    "chest pains" = "chest pains",
    "chest; pain" = "chest; pain",
    "clear throat" = "clear throat",
    "clearing throat" = "clearing throat",
    "clearings throat" = "clearings throat",
    "complaining of cough" = "complaining of cough",
    "cough" = "cough",
    "cough symptom" = "cough symptom",
    "cough symptoms" = "cough symptoms",
    "cough, nos" = "cough, nos",
    "coughing" = "coughing",
    "coughing - function" = "coughing - function",
    "coughing symptom" = "coughing symptom",
    "coughs" = "coughs",
    "d - diarrhea" = "d - diarrhea",
    "d - diarrhoea" = "d - diarrhoea",
    "dark stools" = "dark stools",
    "deglutition disorder" = "deglutition disorder",
    "deglutition disorders" = "deglutition disorders",
    "diarrhea" = "diarrhea",
    "diarrhea nos" = "diarrhea nos",
    "diarrhea running" = "diarrhea running",
    "diarrhea symptom" = "diarrhea symptom",
    "diarrhea symptoms" = "diarrhea symptoms",
    "diarrhea, nos" = "diarrhea, nos",
    "diarrhea, unspecified" = "diarrhea, unspecified",
    "diarrheas" = "diarrheas",
    "diarrhoea" = "diarrhoea",
    "diarrhoea nos" = "diarrhoea nos",
    "diarrhoea symptom" = "diarrhoea symptom",
    "diarrhoea symptoms" = "diarrhoea symptoms",
    "difficult swallowing" = "difficult swallowing",
    "difficult; swallowing" = "difficult; swallowing",
    "difficulties swallowing" = "difficulties swallowing",
    "difficulty in swallowing" = "difficulty in swallowing",
    "difficulty in swallowing nos" = "difficulty in swallowing nos",
    "difficulty swallowing" = "difficulty swallowing",
    "difficulty;swallowing" = "difficulty;swallowing",
    "disorder deglutition" = "disorder deglutition",
    "disorders, deglutition" = "disorders, deglutition",
    "dry heave" = "dry heave",
    "dry heaves" = "dry heaves",
    "dysphagia" = "dysphagia",
    "dysphagia, nos" = "dysphagia, nos",
    "dysphagia, unspecified" = "dysphagia, unspecified",
    "dysphagias" = "dysphagias",
    "emesis" = "emesis",
    "emesis bloody" = "emesis bloody",
    "epigastralgia" = "epigastralgia",
    "epigastric abdominal pain" = "epigastric abdominal pain",
    "epigastric ache" = "epigastric ache",
    "epigastric pain" = "epigastric pain",
    "epigastric; pain" = "epigastric; pain",
    "epigastrium pain" = "epigastrium pain",
    "eructate" = "eructate",
    "eructation" = "eructation",
    "eructation, function" = "eructation, function",
    "eructations" = "eructations",
    "excessive farting" = "excessive farting",
    "excessive passing of gas" = "excessive passing of gas",
    "faecal incontinence" = "faecal incontinence",
    "fart" = "fart",
    "farting" = "farting",
    "farts" = "farts",
    "faucitis" = "faucitis",
    "fecal incontinence" = "fecal incontinence",
    "fecal incontinence nos" = "fecal incontinence nos",
    "feces incontinence" = "feces incontinence",
    "feces incontinence of" = "feces incontinence of",
    "feces; incontinence" = "feces; incontinence",
    "fetor ex ore" = "fetor ex ore",
    "fetor oris" = "fetor oris",
    "finding of vomiting" = "finding of vomiting",
    "flatulence" = "flatulence",
    "flatulence symptom" = "flatulence symptom",
    "flatus" = "flatus",
    "flatus, function" = "flatus, function",
    "foetor ex ore" = "foetor ex ore",
    "foul breath" = "foul breath",
    "foul; breath" = "foul; breath",
    "frequent stools" = "frequent stools",
    "full of wind" = "full of wind",
    "gas passing" = "gas passing",
    "gas raising" = "gas raising",
    "gaseous regurgitation" = "gaseous regurgitation",
    "gaseousness" = "gaseousness",
    "gastric contents; regurgitation" = "gastric contents; regurgitation",
    "gastrointestinal disorder hematemesis" = "gastrointestinal disorder hematemesis",
    "gut pain" = "gut pain",
    "haematemesis" = "haematemesis",
    "haematemesis/vomiting blood" = "haematemesis/vomiting blood",
    "haemorrhage of rectum" = "haemorrhage of rectum",
    "haemorrhage rectal" = "haemorrhage rectal",
    "haemorrhage rectum" = "haemorrhage rectum",
    "halitoses" = "halitoses",
    "halitosis" = "halitosis",
    "heart burn" = "heart burn",
    "heartburn" = "heartburn",
    "heartburn symptom" = "heartburn symptom",
    "heaving" = "heaving",
    "hematemeses" = "hematemeses",
    "hematemesis" = "hematemesis",
    "hematemesis was observed" = "hematemesis was observed",
    "hematemesis/vomiting blood" = "hematemesis/vomiting blood",
    "hemorrhage of rectum" = "hemorrhage of rectum",
    "hemorrhage rectal" = "hemorrhage rectal",
    "hemorrhage rectum" = "hemorrhage rectum",
    "hemorrhage; rectum" = "hemorrhage; rectum",
    "incontinence (fecal)" = "incontinence (fecal)",
    "incontinence bowel" = "incontinence bowel",
    "incontinence faecal" = "incontinence faecal",
    "incontinence fecal" = "incontinence fecal",
    "incontinence of bowel" = "incontinence of bowel",
    "incontinence of faeces" = "incontinence of faeces",
    "incontinence of feces" = "incontinence of feces",
    "incontinence of feces (finding)" = "incontinence of feces (finding)",
    "incontinence of stool" = "incontinence of stool",
    "incontinence stool" = "incontinence stool",
    "incontinence, bowel" = "incontinence, bowel",
    "incontinence, fecal" = "incontinence, fecal",
    "incontinence; fecal" = "incontinence; fecal",
    "incontinence;bowel" = "incontinence;bowel",
    "incontinence;faeces" = "incontinence;faeces",
    "incontinent bowel" = "incontinent bowel",
    "incontinent of bowels" = "incontinent of bowels",
    "incontinent of faeces" = "incontinent of faeces",
    "incontinent of feces" = "incontinent of feces",
    "incontinent of stool" = "incontinent of stool",
    "intestinal gas excretion" = "intestinal gas excretion",
    "involuntary stool" = "involuntary stool",
    "loose bowel motion" = "loose bowel motion",
    "loose bowel motions" = "loose bowel motions",
    "loose bowel movement" = "loose bowel movement",
    "loose stools" = "loose stools",
    "loss of bowel control" = "loss of bowel control",
    "melaena" = "melaena",
    "melena" = "melena",
    "melena (disorder)" = "melena (disorder)",
    "melena/black tarry stools" = "melena/black tarry stools",
    "melenas" = "melenas",
    "nausea" = "nausea",
    "nonspecific chest pain" = "nonspecific chest pain",
    "observation of cough" = "observation of cough",
    "observation of diarrhea" = "observation of diarrhea",
    "observation of diarrhoea" = "observation of diarrhoea",
    "observation of vomiting" = "observation of vomiting",
    "odor breath" = "odor breath",
    "odor of breath" = "odor of breath",
    "odor of breath fetor oris" = "odor of breath fetor oris",
    "odour breath" = "odour breath",
    "of bowel incontinence" = "of bowel incontinence",
    "ozostomia" = "ozostomia",
    "pain abdominal" = "pain abdominal",
    "pain anal" = "pain anal",
    "pain anus" = "pain anus",
    "pain chest" = "pain chest",
    "pain epigastric" = "pain epigastric",
    "pain in chest" = "pain in chest",
    "pain in stomach" = "pain in stomach",
    "pain in the pharynx" = "pain in the pharynx",
    "pain in throat" = "pain in throat",
    "pain pharynx" = "pain pharynx",
    "pain pleural" = "pain pleural",
    "pain thoracic" = "pain thoracic",
    "pain throat" = "pain throat",
    "pain, abdominal" = "pain, abdominal",
    "pain, chest" = "pain, chest",
    "pain, pleuritic" = "pain, pleuritic",
    "pain; abdominal" = "pain; abdominal",
    "pain; anus" = "pain; anus",
    "pain; chest" = "pain; chest",
    "pain; epigastric" = "pain; epigastric",
    "pain; pharynx" = "pain; pharynx",
    "pain; pleura" = "pain; pleura",
    "pain; thorax" = "pain; thorax",
    "pain; throat" = "pain; throat",
    "pain;abdominal" = "pain;abdominal",
    "pain;anal" = "pain;anal",
    "pain;chest" = "pain;chest",
    "pain;epigastric" = "pain;epigastric",
    "pain;throat" = "pain;throat",
    "pains, abdominal" = "pains, abdominal",
    "pains, chest" = "pains, chest",
    "pass wind" = "pass wind",
    "passage of gas by anus" = "passage of gas by anus",
    "passing flatus" = "passing flatus",
    "passing wind" = "passing wind",
    "pharyngeal pain" = "pharyngeal pain",
    "pharynx discomfort" = "pharynx discomfort",
    "pharynx; pain" = "pharynx; pain",
    "pleura; pain" = "pleura; pain",
    "pleural pain" = "pleural pain",
    "pleuralgia" = "pleuralgia",
    "pleuritic chest pain" = "pleuritic chest pain",
    "pleuritic pain" = "pleuritic pain",
    "pleurodynia" = "pleurodynia",
    "pleurodynia nos" = "pleurodynia nos",
    "poor swallowing" = "poor swallowing",
    "pr - bleeding per rectum" = "pr - bleeding per rectum",
    "pr - blood per rectum" = "pr - blood per rectum",
    "prb - rectal bleeding" = "prb - rectal bleeding",
    "proctorrhagia" = "proctorrhagia",
    "pyroses" = "pyroses",
    "pyrosis" = "pyrosis",
    "rb - rectal bleeding" = "rb - rectal bleeding",
    "rectal bleed" = "rectal bleed",
    "rectal bleeding" = "rectal bleeding",
    "rectal blood loss" = "rectal blood loss",
    "rectal discharge incontinent of stool" = "rectal discharge incontinent of stool",
    "rectal discharge incontinent of stool (physical finding)" = "rectal discharge incontinent of stool (physical finding)",
    "rectal haemorrhage" = "rectal haemorrhage",
    "rectal hemorrhage" = "rectal hemorrhage",
    "rectal pain" = "rectal pain",
    "rectorrhagia" = "rectorrhagia",
    "rectum bleeding" = "rectum bleeding",
    "rectum hemorrhage" = "rectum hemorrhage",
    "rectum; hemorrhage" = "rectum; hemorrhage",
    "reflux" = "reflux",
    "reflux, nos" = "reflux, nos",
    "refluxed" = "refluxed",
    "refluxing" = "refluxing",
    "refluxs" = "refluxs",
    "regurgitation" = "regurgitation",
    "regurgitation of gastric content" = "regurgitation of gastric content",
    "regurgitation; gastric contents" = "regurgitation; gastric contents",
    "reported chest pain" = "reported chest pain",
    "retch" = "retch",
    "retching" = "retching",
    "rndx bowel incontinence" = "rndx bowel incontinence",
    "rndx bowel incontinence (diagnosis)" = "rndx bowel incontinence (diagnosis)",
    "rndx diarrhea" = "rndx diarrhea",
    "ructus" = "ructus",
    "runs" = "runs",
    "smelly breath" = "smelly breath",
    "sore symptom throat" = "sore symptom throat",
    "sore symptoms throat" = "sore symptoms throat",
    "sore throat" = "sore throat",
    "sore throat nos" = "sore throat nos",
    "sore throat symptom" = "sore throat symptom",
    "sore throat, nos" = "sore throat, nos",
    "sore throat;" = "sore throat;",
    "sore throats" = "sore throats",
    "sorethroat" = "sorethroat",
    "spitting up" = "spitting up",
    "stomach pain" = "stomach pain",
    "stomatodysodia" = "stomatodysodia",
    "stool black" = "stool black",
    "stool color black" = "stool color black",
    "stool incontinence" = "stool incontinence",
    "stool soiling" = "stool soiling",
    "stool tarry" = "stool tarry",
    "stool(s);black" = "stool(s);black",
    "stool(s);tarry" = "stool(s);tarry",
    "stools loose" = "stools loose",
    "stools.incontinent" = "stools.incontinent",
    "swallowing difficult" = "swallowing difficult",
    "swallowing difficulties" = "swallowing difficulties",
    "swallowing difficulty" = "swallowing difficulty",
    "swallowing disorder" = "swallowing disorder",
    "swallowing disorders" = "swallowing disorders",
    "swallowing; difficult" = "swallowing; difficult",
    "symptoms diarrhea" = "symptoms diarrhea",
    "symptoms vomiting" = "symptoms vomiting",
    "tarry stool" = "tarry stool",
    "tarry stools" = "tarry stools",
    "the runs" = "the runs",
    "the trots" = "the trots",
    "thoracalgia" = "thoracalgia",
    "thoracic pain" = "thoracic pain",
    "thoracodynia" = "thoracodynia",
    "thorax pain" = "thorax pain",
    "thorax painful" = "thorax painful",
    "thorax; pain" = "thorax; pain",
    "throat clearing" = "throat clearing",
    "throat discomfort" = "throat discomfort",
    "throat pain" = "throat pain",
    "throat sore" = "throat sore",
    "throat soreness" = "throat soreness",
    "throat, sore" = "throat, sore",
    "throw up" = "throw up",
    "throwing up" = "throwing up",
    "unable to restrain bowel movement" = "unable to restrain bowel movement",
    "unable to restrain bowel movement (symptom)" = "unable to restrain bowel movement (symptom)",
    "unspecified abdominal pain" = "unspecified abdominal pain",
    "unspecified chest pain" = "unspecified chest pain",
    "vomit" = "vomit",
    "vomited" = "vomited",
    "vomiting" = "vomiting",
    "vomiting blood" = "vomiting blood",
    "vomiting disorder" = "vomiting disorder",
    "vomiting nos" = "vomiting nos",
    "vomiting of blood" = "vomiting of blood",
    "vomiting out blood" = "vomiting out blood",
    "vomiting symptom" = "vomiting symptom",
    "vomiting symptoms" = "vomiting symptoms",
    "vomiting was observed" = "vomiting was observed",
    "vomiting, nos" = "vomiting, nos",
    "vomiting, unspecified" = "vomiting, unspecified",
    "vomiting; blood" = "vomiting; blood",
    "vomiting;blood" = "vomiting;blood",
    "vomits" = "vomits",
    "vomitting blood" = "vomitting blood",
    "vomiturition" = "vomiturition",
    "waterbrash" = "waterbrash",
    "waterbrash symptom" = "waterbrash symptom",
    "watery stool" = "watery stool",
    "watery stools" = "watery stools",
    "wind" = "wind",
    "wind - flatus" = "wind - flatus",
    "wind symptom" = "wind symptom",
    "winding" = "winding",
    "c/o - nausea" = "c/o - nausea",
    "feel sick" = "feel sick",
    "feeling bilious" = "feeling bilious",
    "feeling queasy" = "feeling queasy",
    "feeling sick" = "feeling sick",
    "nausea nos" = "nausea nos",
    "nausea symptom" = "nausea symptom",
    "nausea symptoms" = "nausea symptoms",
    "nausea" = "nausea",
    "nauseas" = "nauseas",
    "nauseated" = "nauseated",
    "nauseating" = "nauseating",
    "nauseous" = "nauseous",
    "observation of nausea" = "observation of nausea",
    "queasy" = "queasy",
    "rndx nausea" = "rndx nausea",
    "sick feeling" = "sick feeling",
    "symptom nausea" = "symptom nausea",
    "symptoms nausea" = "symptoms nausea"
  )

  # To get the list as a list of values only in a regex use
  # paste0(unlist(WordsToNumbers,use.names=F),collapse="|")

  return(Symptoms)
}


#' Convetr words to numbers especially for the histopathology text
#'
#' This function converts words to numbers.
#' @keywords Event extraction
#' @family NLP - Lexicons
#' @export

WordsToNumbers <- function() {
  NumberConv <- list(
    "([Oo]ne) |([Ss]ingle) " = "1",
    #"[Ss]ingle " = "1",
    "[Tt]wo " = "2",
    "[Tt]hree " = "3",
    "[Ff]our " = "4",
    "[Ff]ive " = "5",
    "[Ss]ix " = "6",
    "[Ss]even " = "7",
    "[Ee]ight " = "8",
    "[Nn]ine " = "9",
    "[Tt]en " = "10",
    "[Ee]leven " = "11",
    "[Tt]welve " = "12",
    "[Tt]hirteen " = "13",
    "[Ff]ourteen " = "14",
    "[Ff]ifteen " = "15",
    "[Ss]ixteen " = "16"
  )

  # To get the list as a list of values only in a regex use
  # paste0(unlist(WordsToNumbers,use.names=F),collapse="|")

  return(NumberConv)
}