Hi Sean, Thanks again for the response. I guess its mistake from my side that I dint send the complete text. Did you mean that with the text I sent, the co-reference superscript-1 will be lost?
Also as per your advice, We have created an issue - https://issues.apache.org/jira/browse/CTAKES-459 for measurement FSM changes and attached the modified file changes. Could someone have a look and know your thoughts please? Regards, Gandhi -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Thursday, September 28, 2017 8:21 PM To: dev@ctakes.apache.org Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu> Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Gandhi, I don't recall you sending me that entire snippet of text. I think that I only had your single example sentence. You have discovered one of the quirks of software: "change the data, change the result." Ctakes is a system with many moving parts. Things that precede or follow your original example sentence will change the evaluation of that sentence. With the pipeline you are using and the full note, you should see a number (mine is 4) next to the first "thalomid" in the original example sentence. If you click that number you should see (to the right) 4 instances of "thalomid". Tim can correct me here, but maybe the coreference module ranked the links between "thalomid" as much higher than the rank between "study treatment of thalomid 200mg" and "the treatment of hepatocellular carcinoma" and discarded the encapsulating treatment texts from markables? It is probably more complex than that. > we have also made some code changes in MeasurementFSM.java to identify > certain measurements like '20 mg/m2' which was not identified out of the box. > Should we send the code changes to you so that you can consider the same to > be productized ? Please advise." I don't know if you've noticed the recent emails on the dev list involving Alexandru Zbarcea. Alex has been creating or commenting on Jira items and attaching code for fixes and enhancements. This is a widely used process and is fairly easy to follow. I think that the following links are relevant: Working with issues: https://confluence.atlassian.com/jiracoreserver073/working-with-issues-861257307.html Creating patches: https://confluence.atlassian.com/crucible/creating-patch-files-for-pre-commit-reviews-298977458.html Attaching files: https://confluence.atlassian.com/jiracorecloud/attaching-files-and-screenshots-to-issues-765593805.html I don't know if you have a jira account and permissions for the ctakes project. An administrator may need to set that up for you. Thanks, Sean -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Thursday, September 28, 2017 4:09 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Sean, Thanks for the response. I was able to see the co-reference superscript using the html file that you sent. Interestingly even I was able to generate the sample HTML using piper GUI by having only that single line - " 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. " in the input file. But when I change the input file content with the following lines: "This patient is participating in a Non-IND study; Protocol CG-000424: "Phase I/II of Thalidomide and Epirubicin in Patients with Unresectable or Metastatic Hepatocellular Carcinoma".Information has been received from the investigator regarding an 82 year-old male patient who had gastrointestinal bleeding while on Thalomid, Epirubicin, and Coumadin. He had a past medical history of diverticulosis in 03/02 and a right atrial clot from intraventricular catheter (IVC) for which he was started on Coumadin. During the hospitalization for a right atrial clot in 03/02 hepatocellular carcinoma was first noted and he was referred to an oncologist. 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. He was concomitantly receiving Cardura, Ambien (for insomnia), Megace, Coumadin, and Oxycodone. This patient presented to the emergency room with the chief complaint of hematochezia. He reported noticing bright red blood and small clots mixed in with his stool. On 07/13/02, he was admitted due to gastrointestinal bleed. The physician ordered 2 large bore intravenous lines and planned to transfuse for hematocrit less than 30%. Due to the INR (international normalized ratio) level of 3.0, Coumadin was held. He was also noted to have bilateral lower extremity edema with dyspnea on exertion. On 07/13/02, he had a chest X-ray PA and lateral done that showed no evidence of acute pneumonia or congestive heart failure. On 07/14/02, he underwent an ultrasound which was negative for deep vein thrombosis. This patient did not take Thalomid on the day of his admittance to the hospital, but resumed treatment shortly after with no return of symptoms. On 07/15/02, he was discharged in stable condition. There have been no further reports of bleeding at this time. Thedoctor has assessed the hematochezia as related to Coumadin treatment and previously diagnosed diverticulosis, and not to protocol therapy with Thalomid and Epirubicin.Additional information received from the investigator on 27Aug02 reveals that this male patient began on 07Jun02 two cycles of therapy with Thalidomide and Epirubicin. His post cycle two computed tomography scans revealed increase in size of liver lesion with development of multiple new satellite nodules. On 29Jul02, the investigator removed this patient from protocol for progressive disease and recommended hospice care. After seeking a second opinion from two other institutions, this patient was admitted to hospice on 05Aug02. On 20Aug02, the investigator noted that this patient was suffering worsening fatigue and got tired getting out of his chair. On 25Aug02, this patient died due to disease progression. The investigator assessed the death as not related to study treatment and expected" The co-reference superscript is lost by then. Did you tried with the complete text above by any chance in your piper GUI? Also I guess you did not notice the question on my last post - " Sean, we have also made some code changes in MeasurementFSM.java to identify certain measurements like '20 mg/m2' which was not identified out of the box. Should we send the code changes to you so that you can consider the same to be productized ? Please advise." Regards, Gandhi -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, September 27, 2017 5:53 PM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Gandhi, I am glad that you are feeling better. I don't understand why you aren't getting the same output as me. I just ran your example sentence with your piper with a fresh checkout and get the html below. The css follows. Copy and paste into a file and see if you see the corefs. ///////////////////////////////////////////////////// html, copy into file ///////////////////////////////////////////////// <!DOCTYPE html> <html> <head> <title>OneLiner Output</title> </head> <body> <link rel="stylesheet" href="ctakes.pretty.css" type="text/css" media="screen"> <h2>OneLiner</h2> <i>Text processing finished on: 9 27 2017, 08:15:31</i> <hr> <div id="content"> <p> The patient <span class="AFF_" onClick="iaf('AFF_NL_EVTNL_startedNL_SPC_[before] doc timeNL_NL_')" TIP="Event ">started</span> study <span class="AFF_" onClick="iaf('AFF_NL_EVTNL_treatmentNL_SPC_[before] doc timeNL_NL_PRCNL_treatmentNL_SPC_C0087111NL_SPC_[Therapeutic procedure]NL_SPC_[before] doc timeNL_NL_')" TIP="Event Procedure ">treatment</span><span class="PRC"><sup>•</sup></span> of <span class="AFF_" onClick="iaf('AFF_NL_DRGNL_ThalomidNL_SPC_C0723668NL_SPC_[before] doc timeNL_NL_')" TIP="Drug ">Thalomid</span><span class="DRG"><sup>•</sup></span> <span class="AFF_" onClick="iaf('AFF_NL_EVTNL_200mgNL_SPC_[before] doc timeNL_NL_')" TIP="Event ">200mg</span><span class="UNK" onClick="crf1()"><sup>1</sup></span> ( <span class="GNR_" onClick="iaf('GNR_NL_TMXNL_daysNL_NL_')" TIP="Time ">days</span> 1 - 21 ) , and <span class="AFF_" onClick="iaf('AFF_NL_DRGNL_EpirubicinNL_SPC_C0014582NL_SPC_[before] doc timeNL_NL_')" TIP="Drug ">Epirubicin</span><span class="DRG"><sup>•</sup></span> , 20 mg / m2 ( <span class="GNR_" onClick="iaf('GNR_NL_TMXNL_days 1 , 8NL_NL_')" TIP="Time ">days 1 , 8</span> , and 15 ) on <span class="GNR_" onClick="iaf('GNR_NL_TMXNL_06 / 07 / 02NL_SPC_[CONTAINS] treatmentNL_NL_')" TIP="Time ">06 / 07 / 02</span> for the <span class="AFF_" onClick="iaf('AFF_NL_EVTNL_treatmentNL_SPC_[before] doc timeNL_SPC_06 / 07 / 02 [CONTAINS]NL_NL_PRCNL_treatmentNL_SPC_C0087111NL_SPC_[Therapeutic procedure]NL_SPC_[before] doc timeNL_NL_')" TIP="Event Procedure ">treatment</span><span class="PRC"><sup>•</sup></span> of <span class="AFF_" onClick="iaf('AFF_NL_DISNL_hepatocellular carcinomaNL_SPC_C2239176NL_SPC_[Liver carcinoma]NL_SPC_[before] doc timeNL_NL_')" TIP="Disorder ">hepatocellular </span><span class="AFF_" onClick="iaf('AFF_NL_DISNL_hepatocellular carcinomaNL_SPC_C2239176NL_SPC_[Liver carcinoma]NL_SPC_[before] doc timeNL_NL_EVTNL_carcinomaNL_SPC_[before] doc timeNL_NL_')" TIP="Disorder Event ">carcinoma</span><span class="DIS" onClick="crf1()"><sup>1</sup></span> . <br> </p> </div> <div id="ia"> Annotation Information </div> <script type="text/javascript"> function iaf(txt) { var aff=txt.replace( /AFF_/g,"<br><h3>Affirmed</h3>" ); var neg=aff.replace( /NEG_/g,"<br><h3>Negated</h3>" ); var unc=neg.replace( /UNC_/g,"<br><h3>Uncertain</h3>" ); var unn=unc.replace( /UNN_/g,"<br><h3>Uncertain, Negated</h3>" ); var ant=unn.replace( /ANT/g,"<b>Anatomical Site</b>" ); var dis=ant.replace( /DIS/g,"<b>Disease/ Disorder</b>" ); var fnd=dis.replace( /FND/g,"<b>Sign/ Symptom</b>" ); var prc=fnd.replace( /PRC/g,"<b>Procedure</b>" ); var drg=prc.replace( /DRG/g,"<b>Medication</b>" ); var evt=drg.replace( /EVT/g,"<b>Event</b>" ); var tmx=evt.replace( /TMX/g,"<b>Time</b>" ); var unk=tmx.replace( /UNK/g,"<b>Unknown</b>" ); var spc=unk.replace( /SPC_/g," " ); var prf1=spc.replace( /\[/g,"<i>" ); var prf2=prf1.replace( /\]/g,"</i>" ); var nl=prf2.replace( /NL_/g,"<br>" ); document.getElementById("ia").innerHTML = nl; } function crf1() { document.getElementById("ia").innerHTML = "<br><h3>Coreference Chain</h3>study treatment of Thalomid 200mg<br>the treatment of hepatocellular carcinoma"; } </script></body> </html> ///////////////////////////////////////////////////// css, copy into file named ctakes.pretty.css in same directory as html ///////////////////////////////////////////////// .GNR_ { position: relative; display: inline-block gray; border-bottom: 0.10em solid gray; } .AFF_ { position: relative; display: inline-block green; border-bottom: 0.15em solid green; } .UNC_ { position: relative; display: inline-block gold; border-bottom: 0.16em dotted gold; } .NEG_ { position: relative; display: inline-block red; border-bottom: 0.16em dashed red; } .UNN_ { position: relative; display: inline-block orange; border-bottom: 0.16em dashed orange; } .FND { color: magenta; } .DIS { color: black; } .DRG { color: red; } .PRC { color: blue; } .ANT { color: gray; } .UNK { color: gray; } [TIP] { position: relative; z-index: 2; cursor: pointer; } [TIP]::before, [TIP]::after { visibility: hidden; -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=0)"; filter: progid: DXImageTransform.Microsoft.Alpha(Opacity=0); opacity: 0; pointer-events: none; } [TIP]::before { position: absolute; bottom: 0%; left: 100%; margin-bottom: 5px; padding: 7px; -webkit-border-radius: 3px; -moz-border-radius: 3px; border-radius: 3px; background-color: #000; background-color: hsla(0, 0%, 20%, 0.9); color: #fff; content: attr(TIP); text-align: center; font-size: 14px; line-height: 1.2; } [TIP]:hover::before, [TIP]:hover::after { visibility: visible; -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=100)"; filter: progid: DXImageTransform.Microsoft.Alpha(Opacity=100); opacity: 1; } div#ia { position: fixed; top: 0; right: 0; width: 20%; height: 100%; padding: 10px; overflow: auto; background-color: lightgray; } div#content { width: 79%; height: 100%; padding: 10px; overflow: auto; } -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Wednesday, September 27, 2017 4:40 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Sean, Sorry for the delayed response as I was out of office due to illness. If I don't add BackwardsTimeAnnotator, I don't see any error related to isTraining param. But still couldn't get the superscript co-reference working. Please note that I am using the latest 4.0.1 jars. The piper file and console log messages are as follows: PIPER FILE: // 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 //add org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator // Html output add pretty.html.HtmlTextWriter // XMl writer add FileTreeXmiWriter CONSOLE LOG: 22 Sep 2017 13:59:44 INFO ClearNLPSemanticRoleLabelerAE - Finished initializing 22 Sep 2017 13:59:44 INFO CleartkAnalysisEngine - Starting initializing for Assigning Attributes 22 Sep 2017 13:59:46 INFO CleartkAnalysisEngine - Finished initializing 22 Sep 2017 13:59:46 INFO ModifierExtractorAnnotator - Starting initializing 22 Sep 2017 13:59:46 INFO ModifierExtractorAnnotator - Finished initializing 22 Sep 2017 13:59:46 INFO DegreeOfRelationExtractorAnnotator - Starting initializing 22 Sep 2017 13:59:46 INFO DegreeOfRelationExtractorAnnotator - Finished initializing 22 Sep 2017 13:59:46 INFO LocationOfRelationExtractorAnnotator - Starting initializing 22 Sep 2017 13:59:46 INFO LocationOfRelationExtractorAnnotator - Finished initializing 22 Sep 2017 13:59:46 INFO BackwardsTimeAnnotator - Starting initializing 22 Sep 2017 13:59:46 INFO BackwardsTimeAnnotator - Finished initializing 22 Sep 2017 13:59:46 INFO DocTimeRelAnnotator - Starting initializing 22 Sep 2017 13:59:48 INFO DocTimeRelAnnotator - Finished initializing 22 Sep 2017 13:59:48 INFO EventTimeRelationAnnotator - Starting initializing 22 Sep 2017 13:59:49 INFO EventTimeRelationAnnotator - Finished initializing 22 Sep 2017 13:59:49 INFO EventEventRelationAnnotator - Starting initializing 22 Sep 2017 13:59:51 INFO EventEventRelationAnnotator - Finished initializing 22 Sep 2017 13:59:51 INFO ConstituencyParser - Initializing parser... 22 Sep 2017 13:59:54 INFO RegexSectionizer - Annotating Sections ... 22 Sep 2017 13:59:55 INFO RegexSectionizer - Finished processing 22 Sep 2017 13:59:55 INFO SentenceDetectorAnnotatorBIO - Starting processing ... 22 Sep 2017 13:59:55 INFO SentenceDetectorAnnotatorBIO - Finished processing 22 Sep 2017 13:59:55 INFO ParagraphAnnotator - Annotating Paragraphs ... 22 Sep 2017 13:59:55 INFO ParagraphAnnotator - Finished processing 22 Sep 2017 13:59:55 INFO ParagraphSentenceFixer - Adjusting Sentences overlapping Paragraphs ... 22 Sep 2017 13:59:55 INFO ParagraphSentenceFixer - Finished Processing 22 Sep 2017 13:59:55 INFO ListAnnotator - Annotating Lists ... 22 Sep 2017 13:59:55 INFO ListAnnotator - Finished processing 22 Sep 2017 13:59:55 INFO ListSentenceFixer - Adjusting Sentences overlapping Lists ... 22 Sep 2017 13:59:55 INFO ListSentenceFixer - Finished Processing 22 Sep 2017 13:59:55 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 22 Sep 2017 13:59:55 INFO ContextDependentTokenizerAnnotator - process(JCas) 22 Sep 2017 13:59:55 INFO POSTagger - process(JCas) 22 Sep 2017 13:59:55 INFO Chunker - process(JCas) 22 Sep 2017 13:59:55 INFO ChunkAdjuster - process(JCas) 22 Sep 2017 13:59:55 INFO ChunkAdjuster - process(JCas) 22 Sep 2017 13:59:55 INFO AbstractJCasTermAnnotator - Finding Named Entities ... 22 Sep 2017 13:59:55 INFO AbstractJCasTermAnnotator - Finished processing 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - process dev (JCas) 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:55 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:56 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:56 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:56 INFO DrugMentionAnnotator - -1 22 Sep 2017 13:59:56 INFO ClearNLPDependencyParserAE - Dependency parser starting with thread:pool-2-thread-1 22 Sep 2017 13:59:56 INFO ClearNLPDependencyParserAE - Dependency parser ending with thread:pool-2-thread-1 22 Sep 2017 13:59:56 INFO ClearNLPSemanticRoleLabelerAE - Starting processing ... 22 Sep 2017 13:59:56 INFO ClearNLPSemanticRoleLabelerAE - Finished processing 22 Sep 2017 13:59:56 INFO CleartkAnalysisEngine - Assigning Attributes ... 22 Sep 2017 13:59:56 INFO CleartkAnalysisEngine - Finished Assigning Attributes 22 Sep 2017 13:59:56 INFO ModifierExtractorAnnotator - Starting processing ... 22 Sep 2017 13:59:56 INFO ModifierExtractorAnnotator - Finished processing 22 Sep 2017 13:59:56 INFO DegreeOfRelationExtractorAnnotator - Starting processing ... 22 Sep 2017 13:59:56 INFO DegreeOfRelationExtractorAnnotator - Finished processing 22 Sep 2017 13:59:56 INFO LocationOfRelationExtractorAnnotator - Starting processing ... 22 Sep 2017 13:59:57 INFO LocationOfRelationExtractorAnnotator - Finished processing 22 Sep 2017 13:59:57 INFO BackwardsTimeAnnotator - Starting processing ... 22 Sep 2017 13:59:57 INFO BackwardsTimeAnnotator - Finished processing 22 Sep 2017 13:59:57 INFO DocTimeRelAnnotator - Starting processing ... 22 Sep 2017 13:59:58 INFO DocTimeRelAnnotator - Finished processing 22 Sep 2017 13:59:58 INFO EventTimeRelationAnnotator - Starting processing ... 22 Sep 2017 13:59:59 INFO EventTimeRelationAnnotator - Finished processing 22 Sep 2017 13:59:59 INFO EventEventRelationAnnotator - Starting processing ... 22 Sep 2017 13:59:59 INFO EventEventRelationAnnotator - Finished processing 22 Sep 2017 13:59:59 INFO MaxentParserWrapper - Started processing: test 22 Sep 2017 14:00:02 INFO MaxentParserWrapper - Done parsing: test 22 Sep 2017 14:00:03 INFO MentionClusterCoreferenceAnnotator - Finding Coreferences ... 22 Sep 2017 14:00:03 INFO MentionClusterCoreferenceAnnotator - Finished. 22 Sep 2017 14:00:03 INFO HtmlTextWriter - Writing HTML to D:\Gandhi\ArisG\cTAKES\apache-ctakes-4.0.0\bin_old\test_output\test.txt.pretty.html ... 22 Sep 2017 14:00:03 INFO HtmlTextWriter - Finished Writing 22 Sep 2017 14:00:03 INFO FileTreeXmiWriter - Writing XMI to D:\Gandhi\ArisG\cTAKES\apache-ctakes-4.0.0\bin_old\test_output\test.txt.xmi ... Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 1; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 2; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 4; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 8; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 16; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. Sep 22, 2017 2:00:03 PM org.apache.uima.util.MessageReport decreasingWithTrace(51) WARNING: Message count: 32; Feature org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked multipleReferencesAllowed=false, but it has multiple references. These will be serialized in duplicate. Message count indicates messages skipped to avoid potential flooding. Set FINE logging level for stacktrace. 22 Sep 2017 14:00:03 INFO FileTreeXmiWriter - Finished Writing Sean, we have also made some code changes in MeasurementFSM.java to identify certain measurements like '20 mg/m2' which was not identified out of the box. Should we send the code changes to you so that you can consider the same to be productized ? Please advise. Regards, Gandhi -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, September 22, 2017 6:54 PM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Gandhi, You don't need to add BackwardsTimeAnnotator to your piper. It is added by the TemporalSubPipe.piper. The error that you are seeing regarding training is very strange, but you can try adding this line to the top of the file: set isTraining=false Can you run a sample file with your piper and send me the log statements? It might help me figure out what is going on. > is there any doc or guide on how to start writing our own annotator. There are two example annotators in the ctakes-examples project under the ae/ directory. You can look at those, but I recommend that you look at some information on Uimafit, which can be used to create new annotators: https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org_d_uimafit-2D2.1.0_tools.uimafit.book.pdf&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=OlZ5SUTgU94HjHE8vZDkXv8hjaaa9qEpAlfZjU52Ymk&s=0rIPMY5osSxL4J9gMymmv0bHsBXimd0yb1FmUp4uT-A&e= An introduction to creating Analysis Engines (Annotators) is on page 5. Coding style is individualistic, but below is a rubberstamp that I use to get started: import org.apache.ctakes.core.pipeline.PipeBitInfo; import org.apache.log4j.Logger; import org.apache.uima.UimaContext; import org.apache.uima.analysis_engine.AnalysisEngineProcessException; import org.apache.uima.fit.component.JCasAnnotator_ImplBase; import org.apache.uima.jcas.JCas; import org.apache.uima.resource.ResourceInitializationException; /** * @author SPF , chip-nlp * @version %I% * @since 9/22/2017 */ @PipeBitInfo( name = "Template", description = "For Example.", role = PipeBitInfo.Role.ANNOTATOR ) final public class Template extends JCasAnnotator_ImplBase { static private final Logger LOGGER = Logger.getLogger( "Template" ); /** * {@inheritDoc} */ @Override public void initialize( final UimaContext context ) throws ResourceInitializationException { // Always call the super first super.initialize( context ); // place AE initialization code here } /** * {@inheritDoc} */ @Override public void process( final JCas jCas ) throws AnalysisEngineProcessException { LOGGER.info( "Processing ..." ); // Place AE processing code here LOGGER.info( "Finished." ); } } If you use IntelliJ as your ide you can create a file template with these parameters: #if (${PACKAGE_NAME} && ${PACKAGE_NAME} != "")package ${PACKAGE_NAME};#end import org.apache.ctakes.core.pipeline.PipeBitInfo; import org.apache.log4j.Logger; import org.apache.uima.UimaContext; import org.apache.uima.analysis_engine.AnalysisEngineProcessException; import org.apache.uima.fit.component.JCasAnnotator_ImplBase; import org.apache.uima.jcas.JCas; import org.apache.uima.resource.ResourceInitializationException; #parse("File Header.java") @PipeBitInfo( name = "${NAME}", #if ( ${PROJECT_NAME} != "")description = "For ${PROJECT_NAME}.",#end role = PipeBitInfo.Role.ANNOTATOR ) final public class ${NAME} extends JCasAnnotator_ImplBase { static private final Logger LOGGER = Logger.getLogger( "${NAME}" ); /** * {@inheritDoc} */ @Override public void initialize( final UimaContext context ) throws ResourceInitializationException { // Always call the super first super.initialize( context ); // place AE initialization code here } /** * {@inheritDoc} */ @Override public void process( final JCas jCas ) throws AnalysisEngineProcessException { LOGGER.info( "Processing ..." ); // Place AE processing code here LOGGER.info( "Finished." ); } } -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Friday, September 22, 2017 2:23 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Sean, Thanks again for the detailed response. I still couldn't manage to get superscript-1 co-reference in piper GUI. Also I'm not able to use "BackwardsTimeAnnotator" in piper GUI as it gives me the below error: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator" failed. (Descriptor: <unknown>) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) Caused by: java.lang.IllegalArgumentException: Please specify PARAM_IS_TRAINING - unable to infer it from context at org.cleartk.ml.CleartkAnnotator.initialize(CleartkAnnotator.java:109) Somewhere in old mails it's mentioned that it's because of missing dependencies so I tried adding ClearTkAnnotator with no luck yet. My piper file is as follows: load AdvancedTokenizerPipeline.piper add ContextDependentTokenizerAnnotator add POSTagger load ChunkerSubPipe.piper load DictionarySubPipe.piper add org.apache.ctakes.drugner.ae.DrugMentionAnnotator load AttributeCleartkSubPipe.piper load RelationSubPipe.piper load TemporalSubPipe.piper load CorefSubPipe.piper add org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator add pretty.html.HtmlTextWriter add FileTreeXmiWriter Any suggestion on this? Also I'm using all the latest 4.0.1 cTAKES Jars. Regarding the identification of Names, will dig deep on what you have mentioned. Sorry to ask this as you already mentioned that there are no detailed docs for cTAKES. But is there any doc or guide on how to start writing our own annotator if required? It not, Is there any simple annotator that you would suggest us to look into to get better understanding on annotators for us to proceed further. Thanks in advance. Regards, Gandhi -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Thursday, September 21, 2017 7:59 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Gandhi, > We guess we are missing out on something as we could not find co-references > for "200mg". Should we add anymore piper for this? The piper commands that I sent has everything to obtain coreferences. I use it regularly - it is what I used on your example sentence to get the coreferences that I mentioned. > Also the change mentioned in the thread ... That is a very old thread and I don't think that it applies to what you are trying to do. > We also have a requirement to identify the patient names and sex As James said, ctakes isn't really meant to do this. Ctakes is catered toward extracting clinical data, and to this point names have not fallen into that category. It is more a task for general nlp. There is an opennlp model that can identify names and a few others (I used to see names using GATE). ctakes has wrapped opennlp for other tasks and you should be able to do the same to adapt an engine for names into ctakes. > cTAKES is unable to identify the dates like 20Aug02 or 20/Aug/02 or 06 > / 07 / 02 or 27Aug2002 As Chen mentioned, the BackwardTimeAnnotator module uses an ML model trained on gold data. It isn't perfect. You can add another time annotator on top of this to get some of the more simply formatted date mentions - there are a lot of them out there. Personally I have used jchronic as it can be easily tweaked to recognize medically-relevant temporal expressions relating to surgery, pharmacology, etc. Sean -----Original Message----- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, September 20, 2017 8:50 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] Hi Gandhi, I don't have time to go through all of this right now, but I will try to get to it soon. Make sure that you are running the latest version in trunk. Sean -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Wednesday, September 20, 2017 7:03 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] Hi, Could someone help me out on the below queries please? Regards, Gandhi -----Original Message----- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Tuesday, September 19, 2017 8:51 PM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] 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 - 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=JoUDRZHu91gGMslwknPzTQC_UG2LEBLyOfXR3ikwOL0&s=GzhvIkBu4cgyzYN9n6VLe2rz4sJhJzMxDcWyB0BkqAc&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JoUDRZHu91gGMslwknPzTQC_UG2LEBLyOfXR3ikwOL0&s=9ueuHYwEywok8byBXEkVjmTWiChmaIY3ryB4Pi6ajRo&e= 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFile-2BSubmitter-2BGUI&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JoUDRZHu91gGMslwknPzTQC_UG2LEBLyOfXR3ikwOL0&s=VWIrXrfA2dZ8KHOdoizJo-nTx7nPSy4GDOZ7IxQteIQ&e= > 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. 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. 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