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.jar-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.fi...@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.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>>> 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:bhagwat.pos...@gmail.com>>] Sent: Friday, November 10, 2017 6:13 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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.fi...@childrens.harvard.edu>>> 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:bhagwat.pos...@gmail.com>>] > Sent: Thursday, November 09, 2017 9:06 AM > To: > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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.fi...@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:bhagwat.pos...@gmail.com>>] > > Sent: Wednesday, November 08, 2017 2:41 AM > > To: > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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.natara...@arisglobal.com><mailto:gandhi.natara...@arisglobal.com<mailto:gandhi.natara...@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:bhagwat.pos...@gmail.com>>] > > > Sent: Tuesday, November 07, 2017 3:22 PM > > > To: > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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.natara...@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.com_ > > > > he > > > > al > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=q > > > > S4 > > > > go > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQ > > > > 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.com_ > > > > &d > > > > =D > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZs > > > > tT > > > > py > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQW > > > > 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:bhagwat.pos...@gmail.com>>] > > > > Sent: Friday, November 03, 2017 7:39 PM > > > > To: > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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.fi...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g > > > > > Ta > > > > > o& > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3tr > > > > > 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_TaKVFqO > > > > > nS > > > > > Of > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6Gh > > > > > 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_TaKVFqO > > > > > nS > > > > > Of > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6Gh > > > > > 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:timothy.mil...@childrens.harvard.edu><mailto:timothy.mil...@childrens.harvard.edu<mailto:timothy.mil...@childrens.harvard.edu>>] > > > > > Sent: Monday, October 30, 2017 9:48 AM > > > > > To: > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org><mailto:dev@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:dev@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=qS4goWBT7poplM69z > > > > > y_ > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_ > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCENaERN6B > > > > > 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.natara...@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_3xhKwEW14JZMSdioCoppxeFU& > > > > > > r= > > > > > > He > > > > > > up > > > > > > -I > > > > > > bs > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=E > > > > > > fs > > > > > > fu > > > > > > j3 > > > > > > 7p > > > > > > WN > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4R > > > > > > 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:bhagwat.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
