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> 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] > Sent: Thursday, November 09, 2017 9:06 AM > To: 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 > > > 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] > > Sent: Wednesday, November 08, 2017 2:41 AM > > To: 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> 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] > > > Sent: Tuesday, November 07, 2017 3:22 PM > > > To: 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> 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=qS4 > > > > go > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP > > > > 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=fs67GvlGZstT > > > > py > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCn > > > > 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] > > > > Sent: Friday, November 03, 2017 7:39 PM > > > > To: 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 > > > > > > > > > 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_3xh > > > > > Kw > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa > > > > > o& > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3trfx > > > > > 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_TaKVFqOnS > > > > > Of > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJw > > > > > 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_TaKVFqOnS > > > > > Of > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJw > > > > > 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] > > > > > Sent: Monday, October 30, 2017 9:48 AM > > > > > To: 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> > > > > > Sent: Monday, October 30, 2017 7:24 AM > > > > > To: 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=qS4goWBT7poplM69zy_ > > > > > 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> 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=Efs > > > > > > fu > > > > > > j3 > > > > > > 7p > > > > > > WN > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPg > > > > > > 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] > > > > > > Sent: Monday, October 30, 2017 4:30 PM > > > > > > To: 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
