You can obtain a list of medical terms here link.Then compare them with %in% just like you did before.

It will go something like this:

library(tm)
# set the current script's location as working directory
setwd(dirname(rstudioapi::getSourceEditorContext()$path))


url <- "https://archive.org/stream/azfamilymedicalencyclopedia/A-Z%20Family%20Medical%20Encyclopedia_djvu.txt"
destfile <- "A-Z_Family_Medical_Encyclopedia.txt" # Save it locally with this name

download.file(url, destfile)

file_content <- readLines(destfile, encoding = "UTF-8")

all_text <- paste(file_content, collapse = " ")

words <- unlist(strsplit(all_text, "\W+"))

filtered_words <- words[!tolower(words) %in% stopwords("en")]

filtered_text <- paste(filtered_words, collapse = " ")

# URL for the medical terms word list
medical_terms_url <- "https://raw.githubusercontent.com/glutanimate/wordlist-medicalterms-en/master/wordlist.txt"
medical_terms_file <- "medical_terms.txt"

# Download the medical terms list
download.file(medical_terms_url, medical_terms_file)

# Read the medical terms into a vector
medical_terms <- readLines(medical_terms_file, encoding = "UTF-8")
medical_terms <- tolower(medical_terms)  # Ensure all terms are in lowercase for matching


# Ensure all words in the text are in lowercase
filtered_words_lower <- tolower(filtered_words)

# Keep only words that are in the medical terms list
medical_filtered_words <- filtered_words_lower[filtered_words_lower %in% medical_terms]

unique_medical_filtered_words <-sort(unique(medical_filtered_words))

# do whatever you want with that :)

Results in 282.890 medical related words from 428.875 filtered_words, 10.950 of which being unique.