Below are details of problems I ran across when I tried to run the side effect annotator. It might be too detailed to be of help to you, but perhaps not, or perhaps someone else will chime in who knows more
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Side+Effect Trying to run this aggregate xml descriptor for side effects: desc\ctakes-side-effect\desc\analysis_engine\SideEffectAggregateTAE_UMLS.xml I tried loading that descriptor using CVD. - at load time, DrugCNP2LookupWindow.xml could not be found. I don't see it within cTAKES 4.0. It was part of 3.1. There is a copy at https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ct akes-drug-ner/desc/analysis_engine/ - java.lang.RuntimeException: Attempting to load a FileResource from a jar. The File to be loaded cannot be within a jar.jar:file:/C:/cTAKES/4.0/ap ache-ctakes-4.0.0/lib/ctakes-side-effect-res-4.0.0.jar!/ org/apache/ctakes/sideeffect/lookup/sideEffect_dictionary.txt Sean F. made a change to trunk (revision 1803217) that will likely fix that error. In the meantime, if you are using the cTAKES 4.0 convenience binary, it looks like you can bypass that error by copying that sideeffect subtree to under resources/org/apache/ctakes/sideeffect/ The next thing seems to be that it expects the document to have sections headings and endings in a specific format. There are examples in https://apache.googlesource.com/ctakes/+/branches/ctakes-3.1.0/ctakes-assertion-zoner-res/src/main/resources/org/mitre/medfacts/uima/mayo_sections.xml Here is a snippet of a made-up document that would get recognized. [start section='20104'] Patient reports dizziness after taking celexa and Chlorzoxazone After starting Celexa, patient complains of excess sweating [end section='20104'] Then I'm getting an SQL error when cTAKES is trying to reference a column called FIRST_WORD. That column is in the database for the original dictionary lookup but not the newer fast dictionary lookup. Unfortunately it doesn't look like there is a simple fix or workaround - looks like it will require some digging. -- James On Sun, Oct 29, 2017 at 11:14 PM, Agarwal, Mahesh Kumar < [email protected]> wrote: > Hi James, > > Thank you for your response. I am using version 4.0 and I am running it > through CVD. For example, AggregatePlainFastUMLSProcessor works fine. I > did go through the user installation guide and I (think I) understand the > component dependencies, however, I am unsure how to put the various > components together for side effect detection. Any help will be much > appreciated. > > Best, > Mahesh > > > On Oct 28, 2017, at 9:07 PM, James Masanz <[email protected]> wrote: > > > Which version of cTAKES did you download? > Have you looked at the the User Install Guide: > https://cwiki.apache.org/confluence/display/CTAKES/ > cTAKES+4.0+User+Install+Guide > If so, are you running cTAKES through a CVD, a piper file, a CPE, or are > you launching it in some other way? > > > On Wed, Oct 25, 2017 at 9:23 PM, Agarwal, Mahesh Kumar < > [email protected]> wrote: > >> Hi, >> >> I am new to cTAKES. I have clinical documents and I want to understand >> the side effect of a certain class of drugs. I tried to use the >> SideEffectSentenceAggregate but I keep getting resource initialization >> exceptions. I downloaded the code for the example temporal module provided >> at http://54.68.117.30:8080/index.jsp and it works just fine. >> >> Can anyone please advice what I can do to get this to work? >> >> Best, >> Mahesh >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > >
