R help - Jul 2017 - Extracting sentences with combinations of target words/terms from cancer patient text medical records

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)
  )

Have you looked at the CRAN Natural Language Processing Task View? If not,
why not? If so, why were the resources described there inadequate?

Bert

On Jul 11, 2017 10:49 AM, "Paul Miller via R-help" <r-help at
r-project.org>
wrote:
> 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)
>   )
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

Hi Bert,

Thanks for your reply. It appears that I didn't replace the variable name
"sampletxt" with the argument "x" in my function. I've
corrected that and now my code seems to be working fine.

Paul

________________________________
From: Bert Gunter <bgunter.4567 at gmail.com>

Cc: R-help <r-help at r-project.org>
Sent: Tuesday, July 11, 2017 2:00 PM
Subject: Re: [R] Extracting sentences with combinations of target words/terms
from cancer patient text medical records



Have you looked at the CRAN Natural Language Processing Task View? If not, why
not? If so, why were the resources described there inadequate?

Bert


On Jul 11, 2017 10:49 AM, "Paul Miller via R-help" <r-help at
r-project.org> wrote:

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)
>  )
>
>______________________________ ________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/ listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/
posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
>