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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Input file format for CPE?
Date Mon, 21 Jul 2014 18:52:25 GMT
You may need to modify test_plaintext.xml to use the UMLS-based pipeline if you haven't already.
I think the line:
                <import location="../analysis_engine/AggregatePlaintextProcessor.xml"/>

needs to be changed to use:

AggregatePlaintextUMLSProcessor.xml

I believe you can also make that change in the CPE GUI.

Tim

On 07/21/2014 02:43 PM, Natalia Connolly wrote:
Thanks Tim.  This worked in the sense that it did not crash; however, the output does not
seem to have any actual annotations of diagnoses, medications, etc.  The input text contains
a number of such concepts that had indeed been flagged by CVD; but when I grep for "concept"
or "medfacts" or "cui" in the CPE output there is nothing there.  Would you have any suggestions
for how to "synchronize" the outputs of CVD and CPE?  Both scripts contain the -Dctakes.umlsuser/umlspw
options, so both should have access to UMLS.

Thank you,

Natalia



On Mon, Jul 21, 2014 at 1:36 PM, Miller, Timothy <Timothy.Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.edu>>
wrote:
It looks to me like you want test_plaintext.xml rather than test1.xml. test1.xml seems to
expect CDA-formatted input while test_plaintext.xml can read text files like you have.
Tim


On 07/21/2014 01:30 PM, Natalia Connolly wrote:
Hello,

   I am new to cTAKES.  I am using cTAKES 3.1.  I've been able to run the visual debugger
without any trouble but now I am stuck on running the CPE version, which is what I will really
need as I have a large number of clinical documents to process.

    I loaded test1.xml as the descriptor, and made sure both the input and the output directories
exist.  My single input file in the input directory is just plain text, similar to the "Dr.
Nutritious" example.   However, I am getting the following error:

org.apache.uima.analysis_engine.AnalysisEngineProcessException
CausedBy: org,xml.sax.SAXParseException; lineNumber: 1; columnNumber: 2; Content is now allowed
in Prolog.

   Does this mean that the input file has to be in xml format?  If so, how do I convert plain
text into the format that cTAKES expects?

   Thank you.

   Natalia Connolly






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