[R] Extracting sentences with combinations of target words/terms from cancer patient text medical records

[Paul Miller]

Hello All,

I need some help figuring out how to extract combinations of target words/terms from cancer patient text medical records. I've provided some sample data and code below to illustrate what I'm trying to do. At the moment, I'm trying to extract sentences that contain the word "breast" plus either "metastatic" or "stage IV". 

It's been some time since I used R and I feel a bit rusty. I wrote a function called "sentence_match" that seemed to work well when applied to a single piece of text. You can see that by running the section titled 

"Working code". I thought that it might be possible easily to apply my function to a data set (tibble or df) but that doesn't seem to be the case. My unsuccessful attempt to do this appears in the section titled "Non-working code". 

If someone could help me get my code up and running, that would be greatly appreciated. I'm using a lot of functions from Hadley Wickham's packages, but that's not particularly necessary. Although I have only a few entries in my sample data, my actual data are pretty large. Currently, I'm working with over a million records. Some records contain only a single sentence, but many have several paragraphs. One concern I had was that, even if I could get my code working, it would be too inefficient to handle that volume of data. 

Thanks,

Paul


library(tidyverse)
library(stringr)
library(lubridate)
 
sentence_match <- function(x){
  sentence_extract <- str_extract_all(sampletxt, boundary("sentence"), simplify = TRUE)
  sentence_number <- intersect(str_which(sentence_extract, "breast"), str_which(sentence_extract, "metastatic|stage IV"))
  sentence_match <- str_c(sentence_number, ": ", sentence_extract[sentence_number], collapse = "")
  sentence_match
}
 
#### Working code ####
 
sampletxt <- "This sentence contains the word metastatic and the word breast. This sentence contains no target words."

sentence_match(sampletxt)
 
#### Non-working code ####
 
sampletxt <-
  structure(
    list(
      PTNO = c(1, 2, 2, 2),
      DATE = structure(c(16436, 16436, 16832, 16845), class = "Date"),
      TYPE = c("Progress note", "CAT scan", "Progress note", "Progress note"),
      TVAR = c(
        "This sentence contains the word metastatic. This sentence contains the term stage IV.",
        "This sentence contains no target words. This sentence also contains no target words.",
        "This sentence contains the word metastatic and the word breast. This sentence contains no target words.",
        "This sentence contains the words breast and the term metastatic. This 
sentence contains the word breast and the term stage IV."
      )
    ),
    .Names = c("PTNO", "DATE", "TYPE", "TVAR"),
    class = c("tbl_df",
              "tbl", "data.frame"),
    row.names = c(NA,-4L)
  )
  
sampletxt2 <- group_by_at(sampletxt, vars(PTNO, DATE, TYPE))
sampletxt2 <- 
  sampletxt2 %>%
  mutate(
    EXTRACTED = sentence_match(TVAR)
  )