Hi Sajit, I would say default clinical pipeline is the best place to start for a beginner - https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
Also you got to elaborate what information you are looking for when you say many of the information are irrelevant for you. On Sunday, February 3, 2019, Sajit Kumar <[email protected]> wrote: > 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 > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
