Hi Sean - thanks for such a quick reply. This sounds interesting and something that would help me convey what has been found to non-nlpers. I do all of my processing just through CVD / CPE using the fastUMLSProcessor. So using the nice pipeline creator GUI I have got this far (by importing the existing /clinical/pipeline/DefaultFastPipeline.piper):
// Commands and parameters to create a default plaintext document processing pipeline with UMLS lookup // Load a simple token processing pipeline from another pipeline file # files The text files to be loaded reader org.apache.ctakes.core.cr.TextReader files="C:\Users\arron\Documents\ 200 letters\Epi_Let192.docx" load DefaultTokenizerPipeline.piper // Add non-core annotators add ContextDependentTokenizerAnnotator addDescription POSTagger // Add Chunkers load ChunkerSubPipe.piper // Default fast dictionary lookup add DefaultJCasTermAnnotator // Add Cleartk Entity Attribute annotators load AttributeCleartkSubPipe.piper // HTML Writer // Writes html files with document text and simple markups (Semantic Group, CUI, Negation). # OutputDirectory Directory for all output files. add org.apache.ctakes.core.cc.pretty.html.HtmlTextWriter OutputDirectory Validates fine (yellow button in the pipeline creator), but the option to actually run it (green button) not available yet. I'm guessing I'm missing some pipe bits? In fact, does anyone have an example "start to finish" .piper file? Arron -----Original Message----- From: Finan, Sean [mailto:[email protected]] Sent: 17 July 2017 15:01 To: [email protected] Subject: RE: Filter CVD output? [EXTERNAL] Hi A.S., If you are interested in showing medical terms discovered in text to non-nlpers, you could try adding the html writer to your pipeline. ctakes-core org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java It creates an html file that displays the document text marked with green, red, yellow and orange underlines for affirmed, negated, uncertain, uncertain-negated medical terms. These would be the typical anatomical site, sign/symptom, disease/disorder, medication, procedure mentions. Tooltips appear over the text indicating the semantic type. You can click on the mention and marked-up details will be displayed on the right with polarity, semantic type, cui, document text and preferred text. Overlapping terms are also handled by the tooltips and details panel. The document title (usually filename) is a header at the top of the document, and section headers are displayed larger and normalized. They are also clickable. This of course requires a sectionizer in the pipeline. The html file is named after the document name. html files are saved in a location indicated by the parameter "OutputDirectory". I would like to, in the future, mark up times, lists, and relations. For now, as long as the purpose is displaying mentions to a non-nlper and possibly even passing system output to people that don't have specialized readers (e.g. cvd), the html writer should be useful for a lot of people. Sean -----Original Message----- From: Kean Kaufmann [mailto:[email protected]] Sent: Monday, July 17, 2017 9:30 AM To: [email protected] Subject: Re: Filter CVD output? [EXTERNAL] Hi A.S., Does the "Show Selected Annotations" menu item serve your purposes? https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org_d_uimaj-2Dcurrent_tools.html-23cvd.toolsMenu&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HsoCy31FnpSeRSrfGfy0AvgF2hpkMTGsjlw53mHYzso&s=ESEOutOylgrvMI3vkv4UK7zx7eH82UeCEXZQKKqkvhU&e= On Mon, Jul 17, 2017 at 4:31 AM, Lacey A.S. <[email protected]> wrote: > Hi - I spend a lot of time showing doctors the output of cTakes via > what I have parsed during post processing. Problem being there is not > context of where it is in the letter each term has been pulled from, visually > anyway. > > It would be great if I could sit down and run a letter through the CVD > program and filter the output to just medical mentions? > > Sent from > Nine<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.9folders. > com_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlG > ZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=HsoCy31FnpSeRSrfGfy0AvgF2hpkMTGs > jlw53mHYzso&s=lzGaMHUMam8F2ZpNtTRIilIWHKdm6_2QQD6aU4vQK-E&e= > > >
