Hi Robert,
Thank you for your reply. An attempt to solve this via a regular expression
query is particularly helpful. Unfortunately, I don't have much time to play
around with this just now. Ultimately though, I think I would like to implement
a solution something along the lines of what you have done. I have a book on
regular expressions that I am now starting to read. In the meantime, the code
I'm using is a good way to assess the feasibility of some ideas I'd like to
implement.
The advantage of your approach I think is that it makes fewer passes through
the data. That should make it a lot faster and more efficient than what I've
done. I'm currently working with a little more than 2.5 million text records
and I think that number will only rise. So efficiency really should matter.
I've pasted the latest version of my sample code below. This shows how I'd like
to add the result of the text search as a column in a data frame. It also shows
how I'd like to append the sentence number to each identified sentence. The
single colon that appears where there is no match is not by design. It's
something that I need to tidy.
My sense is that if I used your regular expression as written, I'd lose the
information about the sentence number when I added the result as a column in my
data frame. Presumably, I'd need to collapse the information into a single text
string, and then the numbering would be lost. If you were going to get the
sentence numbers as well, without making several passes through the data like
my code does, how would you go about it?
Thanks,
Paul
library(tidyverse)
library(stringr)
library(lubridate)
sentence_match <- function(x){
sentence_extract <- str_extract_all(x, 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
}
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)
)
sampletxt$EXTRACTED <- sapply(sampletxt$TVAR, sentence_match)
sampletxt$EXTRACTED
> sampletxt$EXTRACTED
[1] ":
"
[2] ":
"
[3] "1: This sentence
contains the word metastatic and the word breast.
"
[4] "1: This sentence contains the words breast and the term metastatic. 2:
This sentence contains the word breast and the term stage IV."
________________________________
From: Robert McGehee <rmcge...@walleyetrading.net>
Cc: "r-help@r-project.org" <r-help@r-project.org>
Sent: Wednesday, July 12, 2017 12:47 PM
Subject: RE: [R] Extracting sentences with combinations of target words/terms
from cancer patient text medical records
Hi Paul,
Sounds like you have your answer, but for fun I thought I'd try solving your
problem using only a regular expression query and base R. I believe this works:
> txt <- "Patient had stage IV breast cancer. Nothing matches this sentence.
> Metastatic and breast match this sentence. French bike champion takes stage
> IV victory in Tour de France."
> pattern <- "([^.?!]*(?=[^.?!]*\\bbreast\\b)(?=[^.?!]*\\b(metastatic|stage
> IV)\\b)(?=[\\s.?!])[^.?!]*[.?!])"
> regmatches(txt, gregexpr(pattern, txt, perl=TRUE, ignore.case=TRUE))[[1]]
[1] "Patient had stage IV breast cancer."
[2] " Metastatic and breast match this sentence."
Cheers, Robert
-----Original Message-----
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Paul Miller via
R-help
Sent: Wednesday, July 12, 2017 8:49 AM
To: Bert Gunter <bgunter.4...@gmail.com>
Cc: R-help <r-help@r-project.org>
Subject: Re: [R] Extracting sentences with combinations of target words/terms
from cancer patient text medical records
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.4...@gmail.com>
Cc: R-help <r-help@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@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@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.
>
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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