Happy New Year cTAKES Community! Hopefully everyone's staying warm. Okay, I did try Matt's suggestion from developer site http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3cced4dccb.126b0%[email protected]%3e but unfortunately it didn't work so I just stepped through the code to see what's going on with how cue words are being used in cTAKES. I verified that the medfacts snapshot jar that contains around 30 txt files for cue words are all being called. So before I tried Matt's recent suggestion I did decompile the medfacts snapshot jar and add the new cue terms to the jar then added it back to cTAKES.... thought it wasn't being recognized but it is. I had updated the speculation text file with 'predictive of' as a new cue term and while stepping through I see that 'predictive of' was recognized as a cue term from the speculation file. The problem is that it gets annotated as 'present' not as 'possible'. That's why I thought the updated cue term wasn't being recognized. I did a quick test using one of the already stated terms(I used 'improbable') from the speculation text file and sure enough the same file that contains the new cue term of 'predictive of' got annotated as 'possible' which has me wondering about the cue model and how it gets generated. So to echo what Tim stated, what does the cue model do? What exactly is that file and how can the contents be viewed and regenerated or updated? Something clearly has to be updated so 'predictive of' gets annotated as 'possible'. I'm so close to getting this resolved so I would appreciate any assistance. Thanks. Regards, Paula From: [email protected] To: [email protected] Subject: Re: cTakes: question on updating cue words Date: Tue, 24 Dec 2013 14:19:46 +0000
Actually, I think Matt's suggestion is a bit out of date -- during development we removed the dependency on the lucene dictionary lookup and now the under development version does read those psv files directly. But this still doesn't help Paula since she's trying to run the current release. I thought Matt or Pei might have some info about whether its possible to modify negation cue words for that release? For example, I can see in the code it uses a "cue model" which can be found in ctakes-assertion-res but it is a binary and I'm not sure what kind. Is there any way to modify that file? Tim On 12/24/2013 12:09 AM, digital paula wrote: Thank you, Pei. I believe I had signed up for the dev list right after Matt posted so I didn't see his email. I will try it out. Merry Christmas to you and everyone on the list. :-) Regards, Paula Date: Mon, 23 Dec 2013 23:42:30 -0500 Subject: Re: cTakes: question on updating cue words From: [email protected] To: [email protected] Paula, Were you able to try Matt's suggestion on dev@? http://mail-archives.apache.org/mod_mbox/ctakes-dev/201312.mbox/%3cced4dccb.126b0%[email protected]%3e On Mon, Dec 23, 2013 at 11:57 AM, digital paula <[email protected]> wrote: Hello again cTAKES Community, I think Tim's away for the holidays since I didn't see any response. Could someone else assist? To reiterate, I'd like to manually update the cue words for the polarity and uncertainty features. Please see below for details. Thanks. Regards, Paula From: [email protected] To: [email protected] Subject: RE: cTakes: question on updating cue words Date: Thu, 19 Dec 2013 16:20:25 -0500 Hi Tim, I just realized that my manual cue word updates didn't take. :-( I updated these two files from the med-facts.i2b21.2-SNAPSHOT.jar, then rebundled and added back to cTAKES: 1. negation_cue_list.txt 2. certainty.txt Is there another file that you know of that needs to be updated? In the cue folder under the jar contains only text files perhaps there's another text file I need to update, would you know what the files would be or what other updates need to be made? Thanks. Regards, Paula Date: Mon, 16 Dec 2013 16:12:29 -0500 From: [email protected] To: [email protected] Subject: Re: cTakes: question on updating cue words Paula, I think to use the released version of ctakes you will have to do what you proposed - modify the jar. The checked in files (*.psv) that you are finding are for the under-development version. Tim On 12/16/2013 03:27 PM, digital paula wrote: Hi Pei, I don't consider this a bug so not sure why a jira ticket is needed, I just need to add 2 cue words wondering if I can do it manually? Exploring a bit, I see there are .psv files in Assertion component in the Cue_Words folder that I updated but it doesn't seem to work. I also added to the Semantic_Classes folder (in Assertion as well), the cue words in the .txt file and that didn't work either. One thing that I haven't tried is updating the cue words in the org.mitre.medfacts.i2b2.cuefiles package for the jar file: medfacts-i2b2-1.2.SNAPSHPOT.jar. That would be a little more work since I need to extract and rebuild jar file and add back to project. I'm kind of on a huge deadline and hoping I can make these changes today so hoping this doesn't require a lot of time to just add a couple cue words. By the way, was is a .psv file? Thanks. Regards, Paula From: [email protected] To: [email protected] Subject: RE: cTakes: question on updating cue words Date: Mon, 16 Dec 2013 19:31:45 +0000 [moved to dev@] Hi Paula, My suggestion would be to open a Jira item so that it could be tracked: https://issues.apache.org/jira/browse/CTAKES (Feel free to create a new account). Even cooler if you could attach the affected files with the patch(diffs) and any tests. --Pei From: digital paula [mailto:[email protected]] Sent: Monday, December 16, 2013 1:30 PM To: [email protected] Subject: cTakes: question on updating cue words Hello again cTAKES Community, I would like to add additional cue words to polarity (for negation) and uncertainty. I would so appreciate if someone can let me know how I can add additional cue words. Thanks. Regards, Paula
