Hi All, I am new to cTakes. I have heard great things about cTakes in processing clinical notes. I have been able to successfully install and launch cTakes applications. However, I have not been able to find enough documentation for the XMI output from these applications such as CPE etc. If anyone can guide me to some documentation to understand the structure of these outputs that would be helpful.
Additionally, I am working on a task where i am interested in extracting the UMLS, SNOMED medical concepts from the clinical notes. However, i see that the output usually has lot of information that is not relevant to my task. I tried my hands at creating a custom pipeline to get rid of this information. But it was throwing an exception. Please find below the script. // *** Piper File *** // Created by Sajit // on February 03, 2019 // Text Files Reader // Reads document texts from text files specified in a provided list. # files The text files to be loaded reader org.apache.ctakes.core.cr.TextReader files=C:\apache-ctakes-4.0.0\testdata\Input\SampleInputRadiologyNotes.txt // UMLS Dictionary Lookup (Old) // Annotates clinically-relevant terms. This is an older, slower dictionary lookup implementation. add org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator // XMI Writer // Writes XMI files with full representation of input text and all extracted information. # OutputDirectory Output directory to write xmi files add org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes OutputDirectory=C:\apache-ctakes-4.0.0\testdata\output This passes the validation but fails to execute. Please tell me if my approach is right or wrong. And is it possible to trim the XMI outputs based on ones need in the cTakes tool. Any suggestion or help is most welcome. Thanks. Regards, Sajit
