RE: ctakes umlsuserapprover authentication error

2015-07-15 Thread Finan, Sean
Hi Stuart, That is strange. Both dictionaries validate the username in the same way, so if it works for one it should work for the other. I am guessing that this problem is repeatable, but I have to ask if you've tested the different dictionaries on different machines or different locations,

RE: periods and the interaction with PTB & Fast Dict Lookup.

2015-07-15 Thread Finan, Sean
Hi Britt, The dictionary should be using ptb tokenization, but I obviously missed a rule and separated the . from the following 2 in the dictionary. I will double-check everything. Sean p.s. if you don’t mind my asking, are you looking into all connective tissue disorders or just Shprintzen?

Re: periods and the interaction with PTB & Fast Dict Lookup.

2015-07-15 Thread britt fitch
Thanks Sean. The other part of the concern is if its reasonable/feasible to alter tokenization rules for things like gene locations. I can work around this in a few ways but if there are other examples of how this might come up in other cases it could be worth looking at a blanket change. Sadly

Re: The SegmentRegexAnnotator of Ytex

2015-07-15 Thread vijay garla
Can you make sure you did everything documented here: https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation I can see from the stack trace that hibernate is not in the classpath (see section 'Unzip YTEX Libraries') Best, VJ On Tue, Jul 14, 2015 at 2:41 AM, Oranit Dror wrote: > T

UmlsConcept subject

2015-07-15 Thread Tomasz Oliwa
Hi, I think there is a regression in the way cTAKES discovers the subject status ("patient", "familiy_member", etc.) of an UmlsConcept. Using cTAKES 3.2.2 and the AggregatePlaintextFastUMLSProcessor in the CVD: 1. "Patient's brother has a myocardial infarction." "myocardial infarction" and "in

RE: UmlsConcept subject

2015-07-15 Thread Chen, Pei
Tomasz, Yes, please please feel free to open a Jira ticket for this. Also, Be sure to include the version of the cTAKES and pipeline you're using. It is possible that the new Subject Classifier isn't classifying this... -Original Message- From: Tomasz Oliwa [mailto:ol...@uchicago.edu] Se

RE: UmlsConcept subject

2015-07-15 Thread Tomasz Oliwa
https://issues.apache.org/jira/browse/CTAKES-369 is open now. Thanks for looking into this. If there is something I could additionally test, let me know.