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
<[email protected]<mailto:[email protected]>>
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
