Thanks again Sean - I now have some nice html files with annotations popping up when hovering over them.
"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." This would be very interesting, and even the ability to mark up user defined annotations / dictionary items would be great. i.e. drug name get picked up, but the units / dose etc would also be really good. All the best, Arron. -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: 17 July 2017 15:01 To: dev@ctakes.apache.org 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:k...@recordsone.com] Sent: Monday, July 17, 2017 9:30 AM To: dev@ctakes.apache.org 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. <a.s.la...@swansea.ac.uk> 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= > > >
