Hi James & Sean, Thanks for your support. Regarding point-1, We don’t have any database or metadata to get the name or sex information. Is it not possible to achieve in cTAKES by any other names? If yes, what other approach will be feasible to implement this along with cTAKES as we need this info very much for our requirement.
Regarding point-2, I will have a check on what you have suggested. But dates analysis is not part of temporal module? Do you mean to say that if we use drug ner module, ContextDependentTokenizerAnnotator will be overwritten for date identifications? Also while using piper GUI to run the analysis, we could see the following message in the console: 21 Sep 2017 00:08:04 INFO EventTimeRelationAnnotator - Starting processing ... Null value found in Feature(<Time-Class->, <NULL>) Could someone brief on this error and how to overcome it? Regards, Gandhi -----Original Message----- From: James Masanz [mailto:masanz.ja...@gmail.com] Sent: Wednesday, September 20, 2017 8:41 PM To: dev@ctakes.apache.org Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] 1) I would typically not use cTAKES for extracting patient names or sex. is there any database or metadata that you can get that information from? 2) Dates are found by the ContextDependentTokenizerAnnotator, which uses DateFSM.java in package org.apache.ctakes.core.fsm.machine. I believe drug ner uses DateParser in org.apache.ctakes.core.util to interpret the date annotations. So you might need to modify both DateFSM and DateParser. On Tue, Sep 19, 2017 at 11:20 AM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Sean, > > Thanks again for the detailed and prompt response. We were able to run > the piper GUI as per your advice. But in the output (The patient > started study treatment of Thalomid 200mg ( days 1 - 21 ) , and > Epirubicin ,20 mg / m2 ( days 1 , 8 , and 15 ) on 06 / 07 / 02 for the > treatment of hepatocellular carcinoma.), we were not able to find > superscript-1 as you mentioned earlier but could find superscript-2, 3 > etc. We guess we are missing out on something as we could not find > co-references for "200mg". Should we add anymore piper for this? > > Also the change mentioned in the thread - http://mail-archives.apache. > org/mod_mbox/ctakes-user/201403.mbox/%3CCAL6WimrJ_mm1+ > xyggbzv62diyuwp0sca9vev8mnhgwe4hsn...@mail.gmail.com%3E is required > for the drug-ner module to identify drug-ner annotations. > > 1) We also have a requirement to identify the patient names and sex > available in narrative texts. Please let us know how to achieve the > same as its not identifying the proper nouns and the relationship with the > patient? > Eg. "This male patient named Tom Hardy aged 35 years is participating > in a Non-IND study" > > 2) cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or > 06 / 07 / 02 or 27Aug2002 as in the below example. Please let us know > how to enhance the system to identify such date patterns. > E.g " On 20Aug02, the investigator noted that this patient was > suffering worsening fatigue and got tired getting out of his chair" > > Regards, > Gandhi > > > -----Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Monday, September 18, 2017 10:02 PM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] > > 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-5Fmm1-2BXyggBZv62diYuWP0ScA9VEV8mNHG > We4hSNHQg-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. 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