Hi Sean,
Many thanks for your reply. Like you say, I see both the lookup descriptors and
all other resources in the projects on the svn server
(https://svn.apache.org/repos/asf/ctakes/trunk/). However, the -res jars that I
get through maven are completely empty, except for their META-INF folder
Hi Jakob,
The -res jars aren't supposed to contain those files. The files should be
placed in the resources/ directory under the ctakes root parallel to lib/.
Can you take me through your checkout / installation and build / run steps? A
list of your svn and maven commands might help me figure
Hi,
I would like to use/extend cTAKES to detect allergies.
In the cTAKES publication (2010)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995668/ there is the mention
that: "Allergies to a given medication are handled by setting the negation
attribute of that medication to ‘is negated’."
However,
Hi Tom,
Are you interested in catching all allergies or just a few specific allergies
for a study? If you are only concerned with a few then there is a (possibly)
simple solution. If you are interested in throwing a wider net then I think
that a new module would need to be created; does anybo
Sean,
It would be a wider net, such that if an allergy is mentioned in the
clinical note, this is captured in the corresponding IdentifiedAnnotation
(or alternatively, if the IdentifiedAnnotation class should not be changed
with a new attribute, in a separate allergy annotation).
This annotator w
Hi Tom,
If the patters are pretty simple, you could just add a few rules on top of the
cTAKES dictionary lookup output. Something of the kind “allergic to
” or “allergies: , , , ...”.
If these patterns are hard to express as rules, you should consider a machine
learning based sequence labeling
Hi Dima, Tom,
I was thinking the same as Dima's first solution. Iterate through the
medication events and see any is included in a phrase as mentioned in Tom's
original email. Each phrase structure would have to be specified beforehand.
However, assigning appropriate CUIs would require havin
Sean and Dima, these are great suggestions, thanks so far.
Sean, when looping over medication events as you say, I can see how it is
possible to take the textspan.Sentence of this MedicationMention, and then
do a regex check for the phrase structure as Dima said.
But instead of textspan.Sentence,
Hi Tom,
It is exactly because the sentence detector splits "KEY:" from "VALUE" that I
didn't suggest using sentences. Instead, I would just iterate over the whole
cas collection of medication events and attempt to match allergy phrases
("allergic to medication") with text the note spanning fr
Thanks, just finished testing and closed the ticket.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
> On Jul 9, 2015, at 3:44 PM, Finan, Sean
> wrote:
>
> Checked in, please give it a test and close the tic
Great, thanks. Any issues or concerns? Possible enhancements? Like the
source, I’m open to change …
From: britt fitch [mailto:britt.fi...@wiredinformatics.com]
Sent: Friday, July 10, 2015 5:29 PM
To: dev@ctakes.apache.org
Subject: Re: dictionary-look-fast fails to handle alternative CUIs
Tha
No issues so far.
I think you are already handling the 1 edge case I could come up with which was
if the numeral portion of the code started with a 0 and it 0 was lost during
the divide step but it looks like you are inserting leading zeros to the
numeral portion if needed with digitCount.
I’l
Hopefully the speed difference will be negligible. It only makes the
conversion at two times: 1. When internally storing a custom dictionary, 2.
When storing discovered CUIs in the cas. Since custom dictionaries are only
read once #1 shouldn’t have any real impact. #2 should require an execut
Hi Tom,
Just for fun I checked "ctakes-allergy" into sandbox. Great title. While too
simple to be really useful, it might serve as a testing point or example for
future endeavors.
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, July
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