Posted by Beverly Shen · Sep 15, 2021 at 8:12 PM

Text/character recognition in Adobe

Is anyone familiar with building queries to run text/character recognition in Adobe pdf documents? Does it require software outside of Adobe?

For context, I need to look through medical records for data like lab results and such based on a medical case definition. If there is a way to do this without manually scrolling through 100 pages, please let me know.

Thank you!

Comments & Events

Patric Prado

You can use R to OCR pdfs. I’ve done this before. Let me know if you need pointers>

https://cran.r-project.org/web/packages/tesseract/vignettes/intro.html

Sep 15, 2021 at 9:56 PM Notified 107 people

Beverly Shen

Thanks, Patric. I'll check this out and let you know if I have any questions.

Sep 21, 2021 at 7:03 PM Notified 107 people

Beverly Shen

Patric

I have some further questions about OCRing pdfs using R, should I post here or email you? Thanks.

Sep 27, 2021 at 8:40 PM Notified 107 people

Patric Prado

It might be good for others to learn if we continue the conversation on here. That being said, it if it get's more complicated - we can definitely schedule a meeting.

THanks

Sep 27, 2021 at 8:43 PM Notified 107 people

Beverly Shen

Sounds good.

Thank you for the link to the OCR tutorial; I was able to read the pdf file into R. Is there a way to then do a search (command F or similar) to look for information within the pdf/png in R. For example, if I read in one page of this made-up medical record

| AST | 458 | Ug/l
| AKP | 394 | Ug/l
| TBil | 7 | Ug/l

Ultrasound nothing special

MRI hepatic nothing unusual

| Hep a | Negative | 4/5/21
| Hep b | Negative | 4/5/21
| Hep c | Positive | 4/5/21
| Igg | negative | 4/5/21

where I want to search for any mentions of "AST" and be directed to "| AST | 458 | Ug/l"

Any pointers greatly appreciated.

Sep 28, 2021 at 4:10 PM Notified 107 people

Jason Wilken

Hi Beverly, not sure you meant to send this to me?

Sep 28, 2021 at 4:34 PM Notified 107 people

Patric Prado

Hey

Jason

these messages get sent to everyone in case there's mutual interest. At the bottom of this thread you can choose unsubscribe me if this doesn't interest you. Thanks

Sep 28, 2021 at 4:38 PM Notified 107 people

Patric Prado

Beverly

please look into agrepl and regular expressions for grabbing lines that contain the words you need. Happy to give you some pointers if you can't find anything.

Sep 28, 2021 at 4:39 PM Notified 107 people

Beverly Shen

I will check out those functions, thanks.

Sep 28, 2021 at 4:43 PM Notified 107 people