Hi Gandhi, > So in this case will be able to see drug attributes in the output XML? As long as you have the DrugMentionAnnotator in your pipeline you should be able to find drug attributes in the xml output file.
> we also saw some code changes needs to be done to use drug-ner module. Is it > still valid? As far as I know there aren't any necessary code changes to get drug ner running. However, I do not normally use drugner so I can't say for certain. > Also you mentioned that the drun-ner module is out of date It can still be used and will produce annotations. All that I meant was that there may not be many people out there using it. It is not part of the default pipeline. > You also mentioned that when you run the sentence, the date was identified. Where and how exactly did you ran it so that we can check the same? I run the following in a piper file because I am interested in a lot of modules (I added drugner just for you): // Advanced Tokenization: Regex sectionization, BIO Sentence Detector (lumper), Paragraphs, Lists load AdvancedTokenizerPipeline.piper add ContextDependentTokenizerAnnotator add POSTagger // Chunkers load ChunkerSubPipe.piper // Default fast dictionary lookup load DictionarySubPipe.piper add org.apache.ctakes.drugner.ae.DrugMentionAnnotator // Cleartk Entity Attributes load AttributeCleartkSubPipe.piper // Relations load RelationSubPipe.piper // Temporal load TemporalSubPipe.piper // Coreferences load CorefSubPipe.piper // Html output add pretty.html.HtmlTextWriter For information on piper files, see https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files I run it in my IDE with: org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G -p <FileAsAbove>.piper -i org/apache/ctakes/examples/notes -o <OutputDir> --user <MyUmlsUser> --pass <MyUmlsPass> You can run it by command line by substituting "org.apache.ctakes.core.pipeline.PiperFileRunner -Xmx3G" with "bin/runPiperFile". You can also run it through a ctakes 4.01 (trunk) gui. See https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI > I'm not able to see any clickable option in HTML output You must have the HtmlTextWriter at the end of your pipeline to produce html files. To keep the xml file output, place "add FileTreeXmiWriter" at the end of the piper. > Apologizes for too many No worries, we are happy to have your interest! Sean -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Saturday, September 16, 2017 7:01 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] Hi Sean, Thanks again for the prompt response. Appreciate your input on adding DrugMentionAnnotator. Actually, we are relying on pretty printer output just to understand the analysis. Our logic to extract disorders and findings are based on the XML file generated by https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_blob_master_ctakes-2Dtemporal-2Ddemo_src_main_java_org_apache_ctakes_web_client_servlet_DemoServlet.java&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_MJKBj93YJdd5aa84dBvqtg6o-BKBn7UcbfF660CEBI&s=g8UzBHRoOyn1hoRABKSC6EtPMvwOSSggviRmWCHKti4&e= So in this case will be able to see drug attributes in the output XML? In one of the old post (https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Duser_201403.mbox_-253CCAL6WimrJ-5Fmm1-2BXyggBZv62diYuWP0ScA9VEV8mNHGWe4hSNHQg-40mail.gmail.com-253E&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_MJKBj93YJdd5aa84dBvqtg6o-BKBn7UcbfF660CEBI&s=iT_1UGR98APO80UaZsaCBHseMqF4M4PfItgokD27r5c&e= ) we also saw some code changes needs to be done to use drug-ner module. Is it still valid? Also you mentioned that the drun-ner module is out of date which means it cannot be used or it may not provide accurate analysis? Also what changes needs to be done to bring it up to date so that we can try the same if you can assist? You also mentioned that when you run the sentence, the date was identified. Where and how exactly did you ran it so that we can check the same? Also regarding you explanation on corefernce, I'm not able to see any clickable option in HTML output. So wanted to understand how can we run and check that too. Apologizes for too many questions as we are just a week old in NLP and cTAKES. Thanks in advance. Regards, Gandhi This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
