Hi Sajit, I m not sure whether creating custom piper is gonna help as I believe default clinical pipeline has the bare minimum but necessary stuff.
You can probably parse the XML and extract out the stuff you want. On Monday, February 4, 2019, Sajit Kumar <kumar.sajit...@gmail.com> wrote: > Hi Gandhi, > > Thanks for your reply. > > Let me elaborate my task. I need to extract the CUIs for the medical > concepts in clinical notes. I believe cTakes can be a very good tool for > this. > I went through the default clinical pipeline. The pipeline is has various > tasks in the pipe such as boundary detection, tokenization, entity > recognition etc. I believe the output XMI document also has sections for > each of these tasks. However, as I am only interested in the CUIs for > medical concepts. I would only be interested in entity recognition and > entity properties in my output. Is it possible to create a custom pipeline > based on this. Or is it possible to turn off the output of unwanted > sections. I hope you understand what I am trying to say. Please advise. > > Also is there any documentation on the structure of cTAKES output files > such as XMI files. > > Looking forward to your response. > > Regards, > Sajit > > On Sun, 3 Feb, 2019, 20:48 gandhi rajan <gandhiraja...@gmail.com wrote: > >> 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 <kumar.sajit...@gmail.com> >> 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 >> !!!" >> >> -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
