Hi Sean, Unfortunately I haven't received it in spam folder too.
On Nov 15, 2017 7:47 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu> wrote: > Hi Bhagwat, > > I sent the email with the output zipped as it contains a javascript file > and those are usually blocked as attachments. Check your spam folder and > see if the server sent it there. > > You can find instructions on building ctakes trunk from code here: > https://cwiki.apache.org/confluence/display/CTAKES/ > cTAKES+4.0+Developer+Install+Guide > > After that just run your piper as you have been. > > Sean > > > -----Original Message----- > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > Sent: Wednesday, November 15, 2017 8:27 AM > To: dev@ctakes.apache.org > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > [SUSPICIOUS] [SUSPICIOUS] > > Hi Sean, > > Thank you for looking at files, I have not yet received the output files > though. > > For an additional information about my output files - I was trying to get > the output using release cTakes-4.0.0 > (apache-ctakes-4.0.0\bin\runPiperFile.bat). > In this release(apache-ctakes-4.0.0\lib), I have copied > ctakes-temporal.jar > created from the source code in ctakes-trunk. With this I could remove the > error from console but tlink is missing in output html. > > With the output file that you have generated could you please also provide > the steps to get the output using the source code in trunk. > > > On 15 November 2017 at 18:20, Finan, Sean <Sean.Finan@childrens.harvard. > edu> > wrote: > > > Hi Bhagwat, > > > > I got your output files, thanks. Tlinks are not present because it comes > > from the ctakes 4.0.0 release, in which the html writer was very > > primitive. It has come a long way since then, and the version in trunk > is > > much more capable. I have emailed you the output files produced by > trunk. > > You can decide whether or not to make the upgrade. > > > > Sean > > > > -----Original Message----- > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com] > > Sent: Wednesday, November 15, 2017 6:49 AM > > To: dev@ctakes.apache.org > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > [SUSPICIOUS] [SUSPICIOUS] > > > > Thank You Sean and Tim for such a useful information. > > > > Now I don't see any error logged on console after replacing > > ctakes-temporal JAR file(Built from source code of trunk and release > 4.0.0 > > as well). > > > > Unfortunately I could not generate TLINK statements in HTML file. > > > > Sean, as you mentioned I am sending my piper file, HTML file and clinical > > note file to your personal email. > > Could you please have a look at it, and provide your thoughts on it. > > > > > > > > On 14 November 2017 at 19:16, Finan, Sean <Sean.Finan@childrens.harvard. > > edu> > > wrote: > > > > > Hi Bhagwat, > > > > > > To build upon what Tim said, not all of the ctakes modules log in the > > > same manor. Some of the more experimental annotators such as those in > > > the temporal module log more 'debug' type events, while some of the > > > standard modules kindly log 'progress' events, such as processing > > > "start" and "finish". In addition, the loggers are typically named > > > after the java class, and sometimes the classes are oddly named. > > > Instead of log messages from a "TimeAnnotator" you are seeing > > > "BackwardsTimeAnnotator", which is appropriate. > > > > > > The apache email bounce will get rid of all attachments, so people on > > > the lists will not be able to get attachments or embedded images. > > > This can be frustrating, but it does add a bit of security for > everybody > > on the list. > > > If you like you can email me your attachments directly - but piper > > > files are plain text that you can just copy and paste into the email. > > > If you are using test data (no phi) then you can send me a zip with > > > the files in your html output directory and I will take a look at them. > > > > > > Also, as Tim noted, capability and behavior of code in trunk are often > > > very different from what you get from a release version. Some things > > > move very quickly in ctakes (and some very slowly). If you are > > > willing to build the code then I always recommend using trunk - > > > sometimes because I just plain forget what the previous release was > > doing. > > > > > > Sean > > > > > > -----Original Message----- > > > From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] > > > Sent: Tuesday, November 14, 2017 7:09 AM > > > To: dev@ctakes.apache.org > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > > [SUSPICIOUS] [SUSPICIOUS] > > > > > > Hi Bhagwat, > > > > > > That error comes from the tlink module, but **it should be possible to > > > create tlinks even if you are getting it**. In fact, for stupid > > > reasons (i.e. my stupidity) you will always see that error when > > > running the tlink annotator. However, I do have a fix for the error, > > > that may help the tlink module somewhat, checked in to trunk about 2 > > > months ago. If you're working off of trunk already, please let me > > > know, because then there is some mistake with my fix. If you're > > > working off of a src release and willing to recompile, it should be a > > reasonably small fix: > > > > > > > > > Replace the existing time annotator model with this one: > > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn. > > > apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal-2Dres_ > > > src_main_resources_org_apache_ctakes_temporal_ae_timeannotator_model.j > > > ar- > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=EPNtkyV_ > > > yUzDNfVUlpTVzGIVBkZsqUVt-4tgYL9SM_8&e= > > > > > > > > > and then update this java file: > > > > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn. > > > apache.org_viewvc_ctakes_trunk_ctakes-2Dtemporal_src_ > > > main_java_org_apache_ctakes_temporal_ae_BackwardsTimeAnnotator.java- > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU > > > &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s= > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e= > > > > > > > > > and recompile, and it should remove the error. > > > > > > > > > Tim > > > > > > > > > ________________________________ > > > From: Bhagwat Posane <bhagwat.pos...@gmail.com> > > > Sent: Tuesday, November 14, 2017 4:16 AM > > > To: dev@ctakes.apache.org > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > > [SUSPICIOUS] > > > > > > Hello Sean, > > > > > > Ok, I understood it now, but in my output, the HTML file doesn't > > > contain TimeAnnotator. below is the part of output: > > > > > > 14 Nov 2017 13:03:19 INFO ContextDependentTokenizerAnnotator - > > > process(JCas) > > > 14 Nov 2017 13:03:19 INFO POSTagger - process(JCas) > > > 14 Nov 2017 13:03:19 INFO Chunker - process(JCas) > > > 14 Nov 2017 13:03:20 INFO ChunkAdjuster - process(JCas) > > > 14 Nov 2017 13:03:20 INFO ChunkAdjuster - process(JCas) > > > 14 Nov 2017 13:03:22 INFO BackwardsTimeAnnotator - Starting > > > processing > > > 14 Nov 2017 13:03:22 INFO BackwardsTimeAnnotator - Finished > > > processing > > > 14 Nov 2017 13:03:22 INFO DocTimeRelAnnotator - Starting processing > > > 14 Nov 2017 13:03:22 INFO DocTimeRelAnnotator - Finished processing > > > 14 Nov 2017 13:03:22 INFO EventTimeRelationAnnotator - Starting > > > processing Null value found in Feature(<Time-Class->, <NULL>) Null > > > value found in Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) Null value found in > > > Feature(<Time-Class->, <NULL>) > > > 14 Nov 2017 13:03:23 INFO EventTimeRelationAnnotator - Finished > > > processing > > > 14 Nov 2017 13:03:23 INFO HtmlTextWriter - Starting processing > > > 14 Nov 2017 13:03:23 INFO HtmlTextWriter - Finished processing > > > > > > I doubt, the blue colored output text is the culprit and causing TLINK > > > not getting generated. To find the cause, I have checked multiple > > > things with no success! > > > However, event-time-relation is captured in xmi with no problem(P.S. > > > Attached). > > > For your reference my piper file is also attached. > > > Could you please have a look at the outputs and guide me to find the > > > root cause or please tell me if you are aware of this behavior. > > > > > > On 13 November 2017 at 18:48, Finan, Sean > <Sean.Finan@childrens.harvard. > > > edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: > > > Hi Bhagwat, > > > > > > The image that you've attached is not coming through, So I cannot see > > > your html file. > > > > > > You should be able to click on any of the underlined terms in the > > > document. When you click on one it will list attributes discovered in > > > the run. For example, clicking on "4:00pm" may display on the right > > > panel "CONTAINS x-ray". > > > > > > Sean > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com>] > > > Sent: Monday, November 13, 2017 3:25 AM > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > > [SUSPICIOUS] > > > > > > Hello Sean, > > > > > > Thank you for the inputs, I have successfully created HTML output. > > > My main aim is to understand context out of clinical note and I hope > > > TLINK statements may help at some extent. > > > I am interested TLINK tag output in HTML, Please correct me if my > > > understanding is not upto the mark. > > > > > > But HTML file doesn't contain any TLINK tags, [Inline images 2] > > > > > > However I can see some tags(copied below) in xmi file which I suppose > > > useful for TLINK tag generation. > > > > > > <relation:RelationArgument xmi:id="8553" id="0" argument="7466" > > > role="Arg2"/> > > > <relation:TemporalTextRelation xmi:id="8282" id="0" category="ENDS-ON" > > > discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0" > > > conditional="false" arg1="8272" arg2="8277"/> > > > <relation:TemporalTextRelation xmi:id="8306" id="0" category="CONTAINS" > > > discoveryTechnique="0" confidence="0.0" polarity="0" uncertainty="0" > > > conditional="false" arg1="8296" arg2="8301"/> > > > > > > > > > I have used TemporalSubPipe.piper file commands to generate the output. > > > > > > //////////////////////////////////////////////////////////// > > > //////////////////////////////////////////////////////////// > > > /////////////////// > > > // Commands and parameters to create a default temporal processing > > > sub-pipeline. This is not a full pipeline. > > > > > > // 'Generic' Events. Use addDescription and let the EventAnnotator > > > set itself up with defaults. > > > addDescription EventAnnotator > > > > > > // Times. There aren't default models, so set specifically add > > > BackwardsTimeAnnotator classifierJarPath=/org/apache/ > > > ctakes/temporal/ae/timeannotator/model.jar > > > > > > // DocTimeRel: the relation bin for Events to the Document Creation > Time. > > > add DocTimeRelAnnotator classifierJarPath=/org/apache/ > > > ctakes/temporal/ae/doctimerel/model.jar > > > > > > // Event - Time binary relations. > > > add EventTimeRelationAnnotator classifierJarPath=/org/apache/ > > > ctakes/temporal/ae/eventtime/model.jar > > > > > > // Event - Event binary relations. > > > add EventEventRelationAnnotator classifierJarPath=/org/apache/ > > > ctakes/temporal/ae/eventevent/model.jar > > > > > > // Html output > > > set OutputDirectory=D:\Bhagwat\HTMLoutput > > > add pretty.html.HtmlTextWriter > > > > > > //XMI output > > > writeXmis D:\Bhagwat\XMI > > > //////////////////////////////////////////////////////////// > > > //////////////////////////////////////////////////////////// > > > /////////////////// > > > > > > Am I missing something? > > > > > > Could you please guide on this. > > > > > > > > > > > > On 10 November 2017 at 18:47, Finan, Sean > <Sean.Finan@childrens.harvard. > > > edu<mailto:sean.fi...@childrens.harvard.edu><mailto: > > > sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@childrens.harvard.e > > > du>>> > > > wrote: > > > Hi Bhagwat, > > > > > > To get html output, you just need to add the html writer and set the > > > output directory. > > > > > > Your #1 should do that. > > > > > > add pretty.html.HtmlTextWriter > > > > > > To set the output directory you can do one of the following: > > > If running from command-line, set it with the -o {directory} option. > > > Or edit the piper file: > > > > > > set OutputDirectory={directory} > > > add pretty.html.HtmlTextWriter > > > > > > or on the same line as add (like your #2) > > > > > > add pretty.html.HtmlTextWriter OutputDirectory={directory} > > > > > > > > > Hopefully at least one of those methods works for you. > > > > > > Sean > > > > > > -----Original Message----- > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > Sent: Friday, November 10, 2017 6:13 AM > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > > [SUSPICIOUS] > > > > > > Hello Sean, > > > > > > Thank you so much, the things you have given works well for me; I > > > could generate the .xmi output file using reader TextReader. > > > And yes, the asterisk marked for "writeXmis" is to highlight for your > > > understanding. > > > > > > The present challenge I am facing is - to parse XMI file and get the > > > required data out of it(e.g. TemporalTextRelation in my case). > > > > > > Is it possible to get the output in HTML format? > > > > > > I have tried to get the HTML output file using below command. > > > > > > 1) add pretty.html.HtmlTextWriter > > > 2) add pretty.html.HtmlTextWriter D:\Bhagwat\output > > > > > > But it does not generate any output file > > > > > > Could you please provide some light on this. > > > > > > > > > On 9 November 2017 at 20:43, Finan, Sean > > > <sean.fi...@childrens.harvard.edu > > > <mailto:sean.fi...@childrens.harvard.edu><mailto: > > > sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@childrens.harvard.e > > > du > > > >>> > > > wrote: > > > > > > > Hi Bhagwat, > > > > > > > > I think that the problem may be reader specification. readFiles > > > > accepts a root directory, not a single file. So you should use > > > > "readFiles D:/Bhagwat" If there is more than data in that directory > > > > then you should copy the data to a different directory and use that. > > > > > > > > readFiles uses the FileTreeReader class. I didn't have the > > > > foresight to accept the possibility of a single file ... I will do > > > > that now before I forget ... I will also add an error message if > > > > the directory > > > is empty. > > > > > > > > You can always use a different reader. I have never used it, but I > > > > think that TextReader might do what you want. The piper line would > > > > be reader TextReader files=D:/Bhagwat/data.txt > > > > > > > > After that any of your specifications for writing xmi files should > > work. > > > > One clarification: "writeXmis" does not have an asterisk. You > > > > probably added one for my benefit. > > > > > > > > Sean > > > > > > > > -----Original Message----- > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > > Sent: Thursday, November 09, 2017 9:06 AM > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > > > [SUSPICIOUS] > > > > > > > > Hello Sean, > > > > > > > > Thank you very much for such a valuable inputs. With these, I could > > > > dive a little deeper in it now. > > > > > > > > I have run the *DefaultFastPipeline.piper* file by adding your given > > > > commands. > > > > > > > > To read clinical note as a input I have added this command > > > > > > > > readFiles D:/Bhagwat/data.txt > > > > > > > > > > > > Execution of this piper file is successful on command line. > > > > to get the output in file or directory, I have tried three ways as > > > > below > > > > > > > > 1) addLast FileTreeXmiWriter OutputDirectory=D:\Bhagwat\output // > > > > in piper > > > > > file > > > > > > > > > > > > > > > > > *2) writeXmis* D:/Bhagwat/output // in piper file > > > > > > > > > > > > > > > > > 3) --xmiOut D:/Bhagwat/output // on command line > > > > > > > > > > > > But it is not generating any output file. please suggest on this. > > > > > > > > > > > > On 8 November 2017 at 18:39, Finan, Sean > > > > <sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@ > > > childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu<mailto: > > > sean.fi...@childrens.harvard.edu>> > > > > > > > > > wrote: > > > > > > > > > Hi Bhagwat, > > > > > > > > > > The ctakes-temporal module has the components needed to generate > > > tlinks. > > > > > Using trunk, the following can be added to the end of the default > > > > > clinical pipeline piper file (or a copy): > > > > > > > > > > load TemporalSubPipe > > > > > > > > > > > > > > > The TemporalSubPipe.piper file contains the following setup to > > > > > create events, times, time relative to document writing > > > > > (doctimerel) > > > and tlinks: > > > > > > > > > > //////////////////////////////////////////////////////////// > > > > > //////////////////////////////////////////////////////////// > > > > > /////////////////// > > > > > // Commands and parameters to create a default temporal processing > > > > > sub-pipeline. This is not a full pipeline. > > > > > > > > > > // 'Generic' Events. Use addDescription and let the > > > > > EventAnnotator set itself up with defaults. > > > > > addDescription EventAnnotator > > > > > > > > > > // Times. There aren't default models, so set specifically add > > > > > BackwardsTimeAnnotator classifierJarPath=/org/apache/ > > > > > ctakes/temporal/ae/timeannotator/model.jar > > > > > > > > > > // DocTimeRel: the relation bin for Events to the Document > > > > > Creation > > > Time. > > > > > add DocTimeRelAnnotator classifierJarPath=/org/apache/ > > > > > ctakes/temporal/ae/doctimerel/model.jar > > > > > > > > > > // Event - Time binary relations. > > > > > add EventTimeRelationAnnotator classifierJarPath=/org/apache/ > > > > > ctakes/temporal/ae/eventtime/model.jar > > > > > > > > > > // Event - Event binary relations. > > > > > add EventEventRelationAnnotator classifierJarPath=/org/apache/ > > > > > ctakes/temporal/ae/eventevent/model.jar > > > > > //////////////////////////////////////////////////////////// > > > > > //////////////////////////////////////////////////////////// > > > > > /////////////////// > > > > > > > > > > To see the code used for tlink detection, search ctakes for the > > > > > EventTimeRelationAnnotator.java and > > > > > EventEventRelationAnnotator.java classes. All piper "add" > commands > > are followed by a class name. > > > > > > > > > > I have a piper file that I use for testing a 'full' ctakes > pipeline: > > > > > > > > > > //////////////////////////////////////////////////////////// > > > > > //////////////////////////////////////////////////////////// > > > > > /////////////////// > > > > > // Advanced Tokenization: Regex sectionization, BIO Sentence > > > > > Detector (lumper), Paragraphs, Lists load > > > > > AdvancedTokenizerPipeline > > > > > > > > > > // Always need these ... > > > > > add ContextDependentTokenizerAnnotator > > > > > add POSTagger > > > > > > > > > > // Chunkers > > > > > load ChunkerSubPipe > > > > > > > > > > // Default fast dictionary lookup > > > > > set minimumSpan=2 > > > > > load DictionarySubPipe > > > > > > > > > > // Cleartk Entity Attributes (negation, uncertainty, etc.) load > > > > > AttributeCleartkSubPipe > > > > > > > > > > // Entity Relations (degree/severity, anatomical location) load > > > > > RelationSubPipe > > > > > > > > > > // Temporal (event, time, dtr, tlink) load TemporalSubPipe > > > > > > > > > > // Coreferences (e.g. patient = he) load CorefSubPipe > > > > > > > > > > // Html output > > > > > add pretty.html.HtmlTextWriter > > > > > > > > > > // XMI output > > > > > writeXmis > > > > > //////////////////////////////////////////////////////////// > > > > > //////////////////////////////////////////////////////////// > > > > > /////////////////// > > > > > > > > > > > > > > > Sean > > > > > > > > > > -----Original Message----- > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > > > Sent: Wednesday, November 08, 2017 2:41 AM > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > Subject: Re: source code of user installation of cTakes. > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > Hi Sean and Tim, > > > > > > > > > > Could you please provide your valuable inputs for below questions: > > > > > > > > > > I am interested in finding the context of clinical notes like if > > > > > any procedure is happened or not. > > > > > I think TLINKS values on web API maybe helpful to get the > > > > > required result, not sure though. Please confirm > > > > > > > > > > I am not able to find the code to generate TLINKS, could you > > > > > please help me locate the code. > > > > > > > > > > On 7 November 2017 at 16:18, Gandhi Rajan Natarajan < > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal > > > > > .com > > > ><mailto:gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@ > > > arisglobal.com>>> wrote: > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > Glad that you got it working. > > > > > > > > > > > > Regarding cTAKES functional questions below, I guess Sean or Tim > > > > > > is the right person to give more info. > > > > > > > > > > > > Regards, > > > > > > Gandhi > > > > > > > > > > > > -----Original Message----- > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > Thanks Gandhi, > > > > > > > > > > > > I have gone through both the links and able to get the results. > > > > > > > > > > > > I am interested in finding the context of clinical notes like if > > > > > > any procedure is happened or not. > > > > > > I think TLINKS values on web API maybe helpful to get the > > > > > > required result, not sure though. Please confirm > > > > > > > > > > > > I am not able to find the code to generate TLINKS, could you > > > > > > please help me locate the code. > > > > > > > > > > > > And also could anybody please guide me to find context out of > > > > > > the note-sentence. > > > > > > > > > > > > On 3 November 2017 at 19:44, Gandhi Rajan Natarajan < > > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@ > > > arisglobal.com><mailto:gandhi.natara...@arisglobal.com<mailto: > > > gandhi.natara...@arisglobal.com>>> wrote: > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > I'm not sure if it will help you. But I extended the code > > > > > > > available in > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.co > > > > > > > m_ > > > > > > > he > > > > > > > al > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c > > > > > > > =q > > > > > > > S4 > > > > > > > go > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNY > > > > > > > mQ > > > > > > > CP > > > > > > > 6r > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk > > > > > > > &s =W yt apFSqEoy1Za7AzcNuuMLQutzXpWTHlzSVl2Gw7zU&e= > > > > > > > to get the XML output and parsed the required mentions for me > > > > > > > like Procedure, Disorder etc. > > > > > > > > > > > > > > You can look at the code here - > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.co > > > > > > > m_ > > > > > > > &d > > > > > > > =D > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlG > > > > > > > Zs > > > > > > > tT > > > > > > > py > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05A > > > > > > > QW Cn wq > > > > > > > n6bOrBk&s=YNBbaimyz_GjWzdMxuIgONTtHRvZiaguYc0pCoNiYjA&e= > > > > > > > gandhirajan/cTAKES/tree/master/cTakes-Rest-Service/ > > > > > > > src/main/java/com/ctakes/nlp and see if it helps. Cheers. > > > > > > > > > > > > > > Regards, > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > > > > > Sent: Friday, November 03, 2017 7:39 PM > > > > > > > To: > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > Thank you Sean and Tim for your support. > > > > > > > > > > > > > > I have followed the links given by Sean and overview by Tim > > > > > > > which is pretty helpful to get the better understanding of > > > > > > > source > > > code. > > > > > > > > > > > > > > I have run ctakes-example project that internally executes > > > > > > > ClinicalPipelineFactory.getDefaultPipeline() method. This has > > > > > > > given results like POS tag, Polarity, etc. > > > > > > > Now, I am more interested in finding Procedure, Medication, > > > > > > > Drug, > > > > etc. > > > > > > > Could you please point me to the code file or help with code > > > > > > > snippet to capture above terms. > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 30 October 2017 at 19:36, Finan, Sean > > > > > > > <sean.fi...@childrens.harvard.edu<mailto:Sean.Finan@ > > > childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu<mailto: > > > sean.fi...@childrens.harvard.edu>> > > > > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > If you are interested in the default clinical pipeline, you > > > > > > > > can look at the wiki here: > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > > > apache. > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy > > > > > > > > _3 > > > > > > > > xh > > > > > > > > Kw > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d > > > > > > > > 4g > > > > > > > > Ta > > > > > > > > o& > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3 > > > > > > > > tr > > > > > > > > fx > > > > > > > > 4P > > > > > > > > oJCYVmL-_RYlSoCOOPf-i_tMs&e= > > > > > > > > Default+Clinical+Pipeline > > > > > > > > For a visual representation of what Tim described. > > > > > > > > > > > > > > > > The AEs used for the ctakes 4.0 default clinical pipeline > > > > > > > > are shown at the bottom of this wiki page: > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > > > apache. > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU& > > > > > > > > r= > > > > > > > > fs > > > > > > > > 67 > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVF > > > > > > > > qO > > > > > > > > nS > > > > > > > > Of > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6 > > > > > > > > Gh Jw s& e= confluence/display/CTAKES/Piper+Files > > > > > > > > The Class names are shown, but not the packages. If you > > > > > > > > have a decent IDE they should be easy to find - for Intellij > > > > > > > > press CTRL-N and type the name of the class. > > > > > > > > > > > > > > > > Another option is to use the Simple Pipeline Fabricator gui > > > > > > > > to look at the available readers and AEs and see what they > > > > > > > > do (and their required inputs). Check the wiki at: > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki. > > > apache. > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU& > > > > > > > > r= > > > > > > > > fs > > > > > > > > 67 > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVF > > > > > > > > qO > > > > > > > > nS > > > > > > > > Of > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6 > > > > > > > > Gh > > > > > > > > Jw s& e= > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator+GUI > > > > > > > > If you launch the gui and let it gather information, you can > > > > > > > > look at the pipe bit names and descriptions (reader, AE). > > > > > > > > If it interests you, click the "add" button (big '+') and on > > > > > > > > the right you will see the path to the source code for that > > > > > > > > bit of the pipeline. Not all AEs > > > > > > > are described ... > > > > > > > > calling all community ... but I think that most are. > > > > > > > > > > > > > > > > Sean > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > From: Miller, Timothy > > > > > > > > [mailto:timothy.mil...@childrens.harvard.edu<mailto:T > > > imothy.mil...@childrens.harvard.edu><mailto:Timothy. > > > mil...@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.e > > > du > > > >>] > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM > > > > > > > > To: > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > > [EXTERNAL] [SUSPICIOUS] > > > > > > > > > > > > > > > > cTAKES is based on Apache UIMA, which is a pipeline-building > > > tool. > > > > > > > > So the output you see in the CVD is the result of many > > > > > > > > different pieces of the pipeline run in succession, and they > > > > > > > > are each in different modules of cTAKES. ctakes-core has the > > > > > > > > most basic elements that will run for every pipeline -- > > > > > > > > tokens, sentences, > > > > etc. > > > > > > > > ctakes-dictionary-lookup-fast is what maps text spans to > > > > > > > > UMLS > > > > > concepts. > > > > > > > ctakes-assertion finds negation status. > > > > > > > > ctakes-chunker creates syntactic chunks and > > > > > > > > ctakes-pos-tagger finds part-of-speech tags for tokens. > > > > > > > > There are many others but I think this covers the basics. In > > > > > > > > general, if you see a type in the CVD that you find > > > > > > > > interesting, your best bet is to grep the code for that type > > > > > > > > and see where it is being created (if you don't want to wait > > > > > > > > for an email > > > > > > > from the list). > > > > > > > > Pipeline components are known as "Analysis Engines" (AEs) in > > > > > > > > UIMA lingo and as a result are often in a package ending in > > .ae. > > > > > > > > Hope this helps you navigate the code! > > > > > > > > Tim > > > > > > > > > > > > > > > > ________________________________________ > > > > > > > > From: Bhagwat Posane <bhagwat.pos...@gmail.com<mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto: > bhagwat > > . > > > pos...@gmail.com>>> > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM > > > > > > > > To: > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:d > > > e...@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > Subject: Re: source code of user installation of cTakes. > > > > > > > > [EXTERNAL] > > > > > > > > > > > > > > > > Thanks Gandhi, for the quick response. > > > > > > > > > > > > > > > > I have source code of cTAKES which is available under > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn. > > > > > > > > apache.org_repos_asf_ctakes_trunk&d=DwIBaQ&c=qS4goWBT7poplM6 > > > > > > > > 9z > > > > > > > > y_ > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_ > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCENaERN > > > > > > > > 6B U3zisHhnM18Wo&e=. I see there are many projects in it. > > > > > > > > > > > > > > > > I am checking user version using > > > > > > > > \CTAKES_HOME\bin\runctakesCVD.bat, > > > > > > > > this opens an UI. I could run analysis engine for a clinical > > > > > > > > note according to the guidelines in the user-install guide.. > > > > > > > > It gives me descent result in the left pane of the UI. > > > > > > > > Now I am looking for the source-code that gives this result > > > > > > > > for a clinical note. Could you please point me to the > > > > > > > > project, where can I see to it in the ctakes-trunk or so. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 30 October 2017 at 16:36, Gandhi Rajan Natarajan < > > > > > > > > gandhi.natara...@arisglobal.com<mailto:Gandhi.Natarajan@ > > > arisglobal.com><mailto:gandhi.natara...@arisglobal.com<mailto: > > > gandhi.natara...@arisglobal.com>>> wrote: > > > > > > > > > > > > > > > > > Hi Bhagwat, > > > > > > > > > > > > > > > > > > The source code of cTAKES is available under > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn. > > > apache. > > > > > > > > > or > > > > > > > > > g_ > > > > > > > > > re > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeF > > > > > > > > > U& > > > > > > > > > r= > > > > > > > > > He > > > > > > > > > up > > > > > > > > > -I > > > > > > > > > bs > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m > > > > > > > > > =E > > > > > > > > > fs > > > > > > > > > fu > > > > > > > > > j3 > > > > > > > > > 7p > > > > > > > > > WN > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz > > > > > > > > > 4R > > > > > > > > > Pg > > > > > > > > > Ch > > > > > > > > > sB > > > > > > > > > LY > > > > > > > > > IC > > > > > > > > > TCQHnrmw&e= > > > > > > > > > asf/ctakes/trunk > > > > > > > > > > > > > > > > > > Regarding the resources to start off, cTAKES official site > > > > > > > > > documentations should be fine. > > > > > > > > > > > > > > > > > > I also feel, mailing list is the one stop shop for all > > > > > > > > > your other detailed queries. > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > > Gandhi > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > > From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com > > <mailto: > > > bhagwat.pos...@gmail.com><mailto:bhagwat.pos...@gmail.com<mailto:bhagw > > > a > > > t.pos...@gmail.com>>] > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM > > > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org > > > ><mailto:dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>> > > > > > > > > > Subject: source code of user installation of cTakes. > > > > > > > > > > > > > > > > > > Hello, > > > > > > > > > > > > > > > > > > I have seen the results of user installation of cTakes , > > > > > > > > > the output is pretty interesting. > > > > > > > > > > > > > > > > > > Can anybody point to the source code of the same? > > > > > > > > > > > > > > > > > > I have just started exploring this project if anybody > > > > > > > > > point me to good resources to understand it thoroughly > > > > > > > > > that will be great > > > > > > > help....!! > > > > > > > > > > > > > > > > > > I have downloaded the developer installation too. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Thanks, > > > > > > > > > Bhagwat Posane > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > Thanks, > > > > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Thanks, > > > > > > > Bhagwat Posane > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Thanks, > > > > > > Bhagwat Posane > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Thanks, > > > > > Bhagwat Posane > > > > > > > > > > > > > > > > > > > > > -- > > > > Thanks, > > > > Bhagwat Posane > > > > > > > > > > > > > > > > -- > > > Thanks, > > > Bhagwat Posane > > > > > > > > > > > > -- > > > Thanks, > > > Bhagwat Posane > > > > > > > > > > > > -- > > > Thanks, > > > Bhagwat Posane > > > > > > > > > > > -- > > Thanks, > > Bhagwat Posane > > > > > > -- > Thanks, > Bhagwat Posane >
