Hi Sean, I ran the batch file and got the following error, so I have something basically wrong, but don't know what. Any help appreciated - Don
My input: bin/runClinicalPipeline -i /tmp/files/CtakesInput --xmiOut /tmp/files/CtakesOutput --user <my userName> --pass <myPass> myUsername and password are correct as I have used them in a number of the cTakes examples and they were verified. The xmiOut directory contains a three short text files, but I don't think the script even got that far. I don't know what the error message means or how to correct it. The output: 27 Feb 2018 13:01:01 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 27 Feb 2018 13:01:01 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 27 Feb 2018 13:01:01 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 27 Feb 2018 13:01:01 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 27 Feb 2018 13:01:01 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 27 Feb 2018 13:01:02 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 27 Feb 2018 13:01:02 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB 27 Feb 2018 13:01:02 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 27 Feb 2018 13:01:02 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml 27 Feb 2018 13:01:02 ERROR PiperFileRunner - Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>) On Tue, Feb 27, 2018 at 8:21 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Don, > > The default clinical pipeline will provide a little more information: > > https://cwiki.apache.org/confluence/display/CTAKES/ > Default+Clinical+Pipeline > > Sean > > > -----Original Message----- > From: Don Flinn [mailto:fl...@alum.mit.edu] > Sent: Tuesday, February 27, 2018 4:16 AM > To: dev@ctakes.apache.org > Subject: Trying to Understand cTAKES [EXTERNAL] > > HI, > I'm new to cTAKES and am trying to understand the product. One of my > goals is to read in medical research documents in a given medical domain, > glean semantic information from them and put the information into a > database, which I can query. I have run through the cTAKES examples and > they seem to go as far as parts of speech (POS). Poking around I found > ClinicalPipelineFactory.java, which computes Subject. Are there other > examples which go further into the semantics? > > Thanks for any help > Don >
