Hi Nick, >file:org/apache/ctakes/dictionary/fast/cTakesHsql.xml
does that file not exist under resources? cTakes shouldn't need anything under that directory to be added to the classpath. I checked the source into trunk this morning, but the zip that you downloaded had everything included. As long as you unzipped in cTakes root the resources, desc and lib should have been properly placed. Sean ________________________________________ From: Nick Nikandish [snika...@emerginghealthit.com] Sent: Wednesday, September 10, 2014 3:06 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K records Hi Sean, I am getting this error: org.apache.uima.resource.ResourceInitializationException: Could not access the resource data at file:org/apache/ctakes/dictionary/fast/cTakesHsql.xml. Where should I add it to the classpath? Thanks, Nick -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Tuesday, September 09, 2014 4:39 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds Just use it with cTakes. Instead of removing other modules from the pipeline, replace the dictionary-lookup with dictionary-lookup-fast. For the desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml , you would modify: <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/> </delegateAnalysisEngine> To be: <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB"> <import location="../../../ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml"/> </delegateAnalysisEngine> That should be it. You can then leave the rest of the module specifications alone. Sean ________________________________________ From: Nick Nikandish [snika...@emerginghealthit.com] Sent: Tuesday, September 09, 2014 4:32 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds Hi Sean, Many thanks, I will try it tomorrow. Do you have any special instruction to run that scrip or I have to use it with cTakes? Thanks, Nick -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Tuesday, September 09, 2014 4:24 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds Hi Nick, I think that the bottleneck is probably the lookup module itself. So, I just sent you a secure email/ftp link. It contains a build of the new dictionary-lookup-fast module. Should you choose to try it, let me know how things turn out. Sean ________________________________________ From: Nick Nikandish [snika...@emerginghealthit.com] Sent: Tuesday, September 09, 2014 4:10 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds Thanks, let me try it. Nick -----Original Message----- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Tuesday, September 09, 2014 4:08 PM To: 'dev@ctakes.apache.org' Subject: RE: Ctakes to process 5000K recoreds If you just need the medication names, you can remove these: <node>ContextDependentTokenizerAnnotator</node> <node>DependencyParser</node> <node>AssertionAnnotator</node> You might be able to get rid of the LvgAnnotator and still get decent results since variations of word form should not affect medication names. I would try with it and without it on a smaller set of files and see if you see a difference. I believe the others are needed by the default configs for medication lookup. For example, POS is used to get phrase type. Phrases are used to remove verb phrases from the lookup and also therefore to keep the lookup windows from getting too big. I'm more familiar with the other types of named entities (diseases, symptoms, etc) than with medications. -----Original Message----- From: Nick Nikandish [mailto:snika...@emerginghealthit.com] Sent: Tuesday, September 09, 2014 3:01 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds James, Do you have any suggestion about running cTakes with minimum annotators that can return Medications in DictionaryLookupAnnotator? Thanks, Nick -----Original Message----- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Tuesday, September 09, 2014 3:05 PM To: 'dev@ctakes.apache.org' Subject: RE: Ctakes to process 5000K recoreds I suspect that when you take out simple segment annotated, nothing is getting processed, and that is why it appears so fast. At least some of the annotators loop through the list of sections/segments, which is why there is a simple segment annotator - so that there is at least one section/segment identified. Are you getting any annotations at all? -----Original Message----- From: Nick Nikandish [mailto:snika...@emerginghealthit.com] Sent: Tuesday, September 09, 2014 2:02 PM To: dev@ctakes.apache.org Subject: RE: Ctakes to process 5000K recoreds Pei, I need the name of the medications for the application that I wrote and uses ctakes.....so I cache the medication in DictionaryLookupAnnotator(in performLookup()) and use them in my program but when I have SimpleSegementAnnotator it just takes forever. After taking SimpleSegementAnnotator out, no medication name in DictionaryLookupAnnotator is returned in the code. So I was wondering if there was a way that I could eliminate SimpleSegementAnnotator but still be able to get the medications name in that class? Nick -----Original Message----- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, September 09, 2014 2:54 PM To: dev@ctakes.apache.org Subject: Re: Ctakes to process 5000K recoreds Nick, When you mean no medication is being annotated, I presume you mean the medication attributes (i.e. dosage, frequency, etc.) are not being annotated? I think the DrugNER needs a list of section names in the config; I think it includes SIMPLE_SEGMENT. I am very surprised that SimpleSegementAnnotator is the bottle neck though; all it does is assume the entire document is a single section called SIMPLE_SEGMENT. Have you tried commenting out the DependencyParser if you're not using those features. --Pei On Tue, Sep 9, 2014 at 2:45 PM, Nick Nikandish <snika...@emerginghealthit.com> wrote: > > Hi there, > > I am using Ctakes to process 5000K free text records where each record has > several medications. > This is the fixed flow that it goes through: > > > <node>SimpleSegmentAnnotator</node> > > <node>SentenceDetectorAnnotator</node> > > <node>TokenizerAnnotator</node> > > <node>LvgAnnotator</node> > > <node>ContextDependentTokenizerAnnotator</node> > > <node>POSTagger</node> > > <node>Chunker</node> > > <node>LookupWindowAnnotator</node> > > <node>DictionaryLookupAnnotatorDB</node> > > <node>DependencyParser</node> > > <node>AssertionAnnotator</node> > > <node>ExtractionPrepAnnotator</node> > > But it takes very very long time to process that many data( maybe a week or > so) when I use SimpleSegmentAnnotator. By eliminating SimpleSegmentAnnotator > the process is very fast but no medication is being anotated. Do you guys > have any suggestion? > > Thanks, > Nick >
