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Posted to dev@ctakes.apache.org by "Finan, Sean" <Se...@childrens.harvard.edu> on 2017/10/30 14:06:59 UTC
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Hi Bhagwat,
If you are interested in the default clinical pipeline, you can look at the wiki here: https://cwiki.apache.org/confluence/display/CTAKES/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://cwiki.apache.org/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://cwiki.apache.org/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.Miller@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 <bh...@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=ZquL0hWuNhJGyujJCmNBTCENaERN6BU3zisHhnM18Wo&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.Natarajan@arisglobal.com> wrote:
> Hi Bhagwat,
>
> The source code of cTAKES is available under
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-Ibs
> Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWN
> oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsBLYIC
> 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.posane@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
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> distributing or taking any action in reliance on the contents of this
> information is strictly prohibited and against the law.
>
--
Thanks,
Bhagwat Posane
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hi Sean,
It is run time error.
I have chosen maven-build for ctakes-core, It gave Build Success message
console.
But when I try to run, It has given Error : Error exists in ctakes-core.
Then I have seen LabValueFinder.java file highlighted with cross sign.
In this file when I hover on putAll() method it shows below error
The method putAll(Map<? extends Annotation,? extends
> List<IdentifiedAnnotation>>) in the type
> Map<Annotation,List<IdentifiedAnnotation>> is not applicable for the
> arguments (Map)
On 21 November 2017 at 18:48, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> Does
> > allCovering.putAll(
> Create a build error or a run error? It shouldn't have a build error.
>
> Sean
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Tuesday, November 21, 2017 5:26 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> Thank you very much for the help, finally I am able to generate the Html
> output file with tlink statement using piper file.
>
> Although I have taken latest trunk update, in LabValuFinder.java the
> putAll() method giving build error. this was the culprit. for me to get it
> worked, I have commented the code and run it.
>
> @SuppressWarnings( { "rawtypes", "unchecked" } ) // hold my beer and watch
> this...
> static private Map<Annotation, List<IdentifiedAnnotation>>
> createCoveringMap( final JCas jCas,
>
> final List<Class<? extends Annotation>> coveredClasses,
>
> final List<Class<? extends IdentifiedAnnotation>> coveringClasses ) {
> final Map<Annotation, List<IdentifiedAnnotation>> allCovering = new
> HashMap<>();
> // for ( Class covered : coveredClasses ) {
> // for ( Class covering : coveringClasses ) {
> // allCovering.putAll( JCasUtil.indexCovering( jCas, covered,
> covering ) );
> // }
> // }
> return allCovering;
> }
>
> I think this needs to be fixed, not sure though.
>
> I have few more quires I will write it in separate thread.
>
>
> On 20 November 2017 at 20:09, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Bhagwat,
> >
> > I have no idea why that isn't working. Ctakes-examples should have
> > everything in its classpath.
> >
> > Ok, try this instead:
> >
> > Update to the latest version of trunk.
> >
> > On the left or right you may see a "maven projects" tab. If you don’t
> you
> > can activate it using the menubar: View > Tool Windows > Maven Projects.
> >
> > Expand the "Maven Projects" tab. You should see a list or tree with
> > "profiles" at the top, followed by "Apache cTAKES" and then ctakes
> modules.
> >
> > Expand "profiles" and click the box next to runPiperGui. If you don't
> see
> > "runPiperGui" then you don't really have the latest version of trunk.
> >
> > Expand "Apache ctakes" and double-click clean. When Clean has finished
> > double-click "compile". You should see ctakes compile for a while and
> > then a gui should pop up. This is the Piper File Submitter. Follow the
> > instructions on the wiki, pointing to your piper file, etc.
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.
> apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> p8r3qe3ZhAJ2sfB9BKxtO6xgHUdUk0WWaB2A57OEJLs&s=pRJ81R6rCn_
> PT5H7O4cV9lSE4CMegjcRUNKIPNkqZZo&e=
> > Piper+File+Submitter+GUI
> >
> > Sean
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Monday, November 20, 2017 7:12 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hello Sean,
> >
> > I have installed intellij IDE imported maven project and compiled it
> using
> > cTAKES+4.0+Developer+Install+Guide.
> >
> > Then I have followed the steps you have given for running the piper file
> > using IDE
> >
> > I set the following in Run Configuration
> >
> > Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
> > VM Options: -Xmx3G
> > Working Directory: path/to/your/ctakes/
> > Use Classpath of module: ctakes-examples
> >
> > Arguments:
> > -p Path/to/your/PiperFile.piper
> > --user yourUmlUsername
> > --pass yourUmlsPassword
> >
> > But I am getting this error : Could not find or load main class
> > org.apache.ctakes.core.pipeline.PiperFileRunner
> > Could you please provide some inputs on it.
> >
> > On 17 November 2017 at 22:04, Finan, Sean <Sean.Finan@childrens.harvard.
> > edu>
> > wrote:
> >
> > > Hi Bhagwat,
> > >
> > > It is a little late, but I just checked in a maven profile that will
> > start
> > > the piper file submitter gui. To use it:
> > >
> > > 1. update your local sandbox with trunk
> > > 2. There should be a maven tab somewhere in eclipse ...
> > > 3. On the maven tab, enable the profile "runPiperGui"
> > > 4. run maven compile
> > >
> > > The compilation stage should start, and near the end the piper gui will
> > > pop up.
> > >
> > > Sean
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > Sent: Friday, November 17, 2017 1:29 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > > [SUSPICIOUS] [SUSPICIOUS]
> > >
> > > Hi Sean,
> > >
> > > I am using Eclipse Mars IDE.
> > > Could you please tell me how to to set up an ide to run directly using
> > the
> > > source code.
> > >
> > > On 16 November 2017 at 20:23, Finan, Sean
> <Sean.Finan@childrens.harvard.
> > > edu>
> > > wrote:
> > >
> > > > Hi Bhagwat,
> > > >
> > > > I think that you are close, but that workflow won't pan out.
> > > >
> > > > If you want to run just like the ctakes release, run maven package,
> > > > then go to the target/ directory in -distribution and unzip one of
> the
> > > > created -bin files to another directory and then use that directory
> > > > just like you would the ctakes release. Please note that you will
> > > > need to copy the ctakes dictionary from your source into that
> > > installation.
> > > >
> > > > If you are familiar with running from source that would be much
> easier.
> > > > Are you using an IDE? It is very easy to set up an ide to run
> > > > directly using the source code, which means that you don't have to
> > > > both with the long package and copy process.
> > > >
> > > >
> > > > Sean
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > > Sent: Thursday, November 16, 2017 4:17 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > > > [SUSPICIOUS] [SUSPICIOUS]
> > > >
> > > > Hello Sean,
> > > >
> > > > Sorry to say but I haven't received any files, hope you are sending
> it
> > > > on my personal email.
> > > > Will it be possible to share it through dropbox or google drive?
> > > >
> > > > I have followed the steps provided on the link.
> > > > After building ctakes-trunk, I have tried to run the piper file using
> > > > ctake-distribution module where runpiper.bat file present, it means
> my
> > > > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
> > > >
> > > > I ran the command
> > > >
> > > > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> > > > D:\DefaultFastPipeline.piper --user USER --pass PASS
> > > >
> > > > it is giving following error:
> > > >
> > > > Error: Could not find or load main class org.apache.ctakes.core.
> > > > pipeline.PiperFileRunner
> > > >
> > > > On 15 November 2017 at 22:07, Finan, Sean
> > <Sean.Finan@childrens.harvard.
> > > > edu>
> > > > wrote:
> > > >
> > > > > I just sent it 2 more times ...
> > > > >
> > > > > -----Original Message-----
> > > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > > > Sent: Wednesday, November 15, 2017 11:20 AM
> > > > > To: dev@ctakes.apache.org
> > > > > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > > > > [SUSPICIOUS] [SUSPICIOUS]
> > > > >
> > > > > Hi Sean,
> > > > >
> > > > > Unfortunately I haven't received it in spam folder too.
> > > > >
> > > > > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > > > > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.
> apache.
> > > > > > or
> > > > > > g_
> > > > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14
> > > > > > JZ
> > > > > > MS
> > > > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=JsLzIX
> > > > > > rN
> > > > > > wY
> > > > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=
> 70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > > > > m0
> > > > > > O1
> > > > > > 1vwvOMhuk&e=
> > > > > > cTAKES+4.0+Developer+Install+Guide
> > > > > >
> > > > > > After that just run your piper as you have been.
> > > > > >
> > > > > > Sean
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > > > > _m
> > > > > > > > od
> > > > > > > > el.j
> > > > > > > > ar-
> > > > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCop
> > > > > > > > px eF U&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
> > > > > > > > .j
> > > > > > > > av
> > > > > > > > a-
> > > > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdio
> > > > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=
> > > > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > > > > >
> > > > > > > >
> > > > > > > > and recompile, and it should remove the error.
> > > > > > > >
> > > > > > > >
> > > > > > > > Tim
> > > > > > > >
> > > > > > > >
> > > > > > > > ________________________________
> > > > > > > > From: Bhagwat Posane <bh...@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 ContextDependentTokenizerAnnot
> ator
> > > > > > > > -
> > > > > > > > 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<ma...@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.posane@gmail.com
> <mailto:
> > > > > > > > bhagwat.posane@gmail.com>]
> > > > > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.h
> > > > > > > > ar
> > > > > > > > va
> > > > > > > > rd.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.posane@gmail.com
> <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.h
> > > > > > > > ar
> > > > > > > > va
> > > > > > > > rd.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.posane@gmail.com
> > <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><mailto:d
> > > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.
> edu
> > > > > <mailto:
> > > > > > > > Sean.Finan@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.posane@gmail.com
> > > <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><mailto
> > > > > > > > > > :d
> > > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@ar
> > > > > > > > > > is
> > > > > > > > > > gl
> > > > > > > > > > obal
> > > > > > > > > > .com
> > > > > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.
> Nataraj
> > > > > > > > >an
> > > > > > > > >@
> > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><mail
> > > > > > > > > > > to
> > > > > > > > > > > :d
> > > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@
> > > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<
> mailto:
> > > > > > > > Gandhi.Natarajan@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__g
> > > > > > > > > > > > it
> > > > > > > > > > > > hu
> > > > > > > > > > > > b.co
> > > > > > > > > > > > m_
> > > > > > > > > > > > he
> > > > > > > > > > > > al
> > > > > > > > > > > > thnlp_examples_tree_master_
> ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > > > > Dw
> > > > > > > > > > > > IB
> > > > > > > > > > > > aQ&c
> > > > > > > > > > > > =q
> > > > > > > > > > > > S4
> > > > > > > > > > > > go
> > > > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTp
> > > > > > > > > > > > yI
> > > > > > > > > > > > is
> > > > > > > > > > > > CYNY
> > > > > > > > > > > > mQ
> > > > > > > > > > > > CP
> > > > > > > > > > > > 6r
> > > > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_
> TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > > > > qn
> > > > > > > > > > > > 6b OrBk &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__g
> > > > > > > > > > > > it
> > > > > > > > > > > > hu
> > > > > > > > > > > > b.co
> > > > > > > > > > > > m_
> > > > > > > > > > > > &d
> > > > > > > > > > > > =D
> > > > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > > > > fs
> > > > > > > > > > > > 67
> > > > > > > > > > > > GvlG
> > > > > > > > > > > > Zs
> > > > > > > > > > > > tT
> > > > > > > > > > > > py
> > > > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&
> m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > > > > Of
> > > > > > > > > > > > qj
> > > > > > > > > > > > R05A
> > > > > > > > > > > > QW Cn wq
> > > > > > > > > > > > n6bOrBk&s=YNBbaimyz_GjWzdMxuIgONTtHRvZiaguYc0pCoNi
> YjA&
> > > > > > > > > > > > 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.posane@gmail.
> com
> > > > > <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><ma
> > > > > > > > > > > > il
> > > > > > > > > > > > to
> > > > > > > > > > > > :d
> > > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.
> edu
> > > > > <mailto:
> > > > > > > > Sean.Finan@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_
> > > > > > > > > > > > > _c
> > > > > > > > > > > > > wiki
> > > > > .
> > > > > > > > apache.
> > > > > > > > > > > > > org_confluence_display_CTAKES_
> &d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > > > > op
> > > > > > > > > > > > > lM
> > > > > > > > > > > > > 69zy
> > > > > > > > > > > > > _3
> > > > > > > > > > > > > xh
> > > > > > > > > > > > > Kw
> > > > > > > > > > > > > EW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > > > > pK
> > > > > > > > > > > > > Gd
> > > > > > > > > > > > > 4f7d
> > > > > > > > > > > > > 4g
> > > > > > > > > > > > > Ta
> > > > > > > > > > > > > o&
> > > > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk
> &s=VdNz
> > > > > > > > > > > > > 5x
> > > > > > > > > > > > > 7X
> > > > > > > > > > > > > XCD3
> > > > > > > > > > > > > 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_
> > > > > > > > > > > > > _c
> > > > > > > > > > > > > wiki
> > > > > .
> > > > > > > > apache.
> > > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioC
> > > > > > > > > > > > > op
> > > > > > > > > > > > > px
> > > > > > > > > > > > > eFU&
> > > > > > > > > > > > > r=
> > > > > > > > > > > > > fs
> > > > > > > > > > > > > 67
> > > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd
> 4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > > dL
> > > > > > > > > > > > > _T
> > > > > > > > > > > > > aKVF
> > > > > > > > > > > > > qO
> > > > > > > > > > > > > nS
> > > > > > > > > > > > > Of
> > > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=
> 1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > > lf
> > > > > > > > > > > > > 24
> > > > > > > > > > > > > gMo6 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_
> > > > > > > > > > > > > _c
> > > > > > > > > > > > > wiki
> > > > > .
> > > > > > > > apache.
> > > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioC
> > > > > > > > > > > > > op
> > > > > > > > > > > > > px
> > > > > > > > > > > > > eFU&
> > > > > > > > > > > > > r=
> > > > > > > > > > > > > fs
> > > > > > > > > > > > > 67
> > > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd
> 4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > > dL
> > > > > > > > > > > > > _T
> > > > > > > > > > > > > aKVF
> > > > > > > > > > > > > qO
> > > > > > > > > > > > > nS
> > > > > > > > > > > > > Of
> > > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=
> 1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > > lf
> > > > > > > > > > > > > 24
> > > > > > > > > > > > > gMo6
> > > > > > > > > > > > > Gh
> > > > > > > > > > > > > Jw s& e=
> > > > > > > > > > > > > confluence/display/CTAKES/
> Simple+Pipeline+Fabricator
> > > > > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu
> <mailto:
> > > > > > > > > > > > > T
> > > > > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@
> childrens.h
> > > > > > > > ar
> > > > > > > > va
> > > > > > > > rd.e
> > > > > > > > du
> > > > > > > > >>]
> > > > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > > > > To:
> > > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><
> > > > > > > > > > > > > ma
> > > > > > > > > > > > > il
> > > > > > > > > > > > > to:d
> > > > > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<
> > mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> > > <mailto:
> > > > > > bhagwat
> > > > > > > .
> > > > > > > > posane@gmail.com>>>
> > > > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > > > > To:
> > > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><
> > > > > > > > > > > > > ma
> > > > > > > > > > > > > il
> > > > > > > > > > > > > to:d
> > > > > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > > > > T7
> > > > > > > > > > > > > po
> > > > > > > > > > > > > plM6
> > > > > > > > > > > > > 9z
> > > > > > > > > > > > > y_
> > > > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=
> Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > > > > TK
> > > > > > > > > > > > > -
> > > > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> x6674h&m=Efsfuj37pWNoR
> > > > > > > > > > > > > _
> > > > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&
> s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:
> Gandhi.Natara
> > > > > > > > > > > > > ja
> > > > > > > > > > > > > n@
> > > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<
> mailto:
> > > > > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > > > > >
> > > > > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > > > > https://urldefense.proofpoint.
> com/v2/url?u=https-3
> > > > > > > > > > > > > > A_
> > > > > > > > > > > > > > _svn
> > > > > .
> > > > > > > > apache.
> > > > > > > > > > > > > > or
> > > > > > > > > > > > > > g_
> > > > > > > > > > > > > > re
> > > > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdi
> > > > > > > > > > > > > > oC
> > > > > > > > > > > > > > op
> > > > > > > > > > > > > > pxeF
> > > > > > > > > > > > > > U&
> > > > > > > > > > > > > > r=
> > > > > > > > > > > > > > He
> > > > > > > > > > > > > > up
> > > > > > > > > > > > > > -I
> > > > > > > > > > > > > > bs
> > > > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > > > > x6
> > > > > > > > > > > > > > 67
> > > > > > > > > > > > > > 4h&m
> > > > > > > > > > > > > > =E
> > > > > > > > > > > > > > fs
> > > > > > > > > > > > > > fu
> > > > > > > > > > > > > > j3
> > > > > > > > > > > > > > 7p
> > > > > > > > > > > > > > WN
> > > > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&
> s=O0hR4sqek-qxWLs
> > > > > > > > > > > > > > 6i
> > > > > > > > > > > > > > ya
> > > > > > > > > > > > > > qEJz
> > > > > > > > > > > > > > 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.posane@gmail.com
> > > > > > > <mailto:
> > > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mail
> > > > > > > > to
> > > > > > > > :b
> > > > > > > > hagw
> > > > > > > > a
> > > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > > > > To:
> > > > > > > > > > > > > > dev@ctakes.apache.org<mailto:d
> ev@ctakes.apache.org
> > > > > > > > ><ma...@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
> > > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Thanks,
> > > > Bhagwat Posane
> > > >
> > >
> > >
> > >
> > > --
> > > Thanks,
> > > Bhagwat Posane
> > >
> >
> >
> >
> > --
> > Thanks,
> > Bhagwat Posane
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Bhagwat,
Does
> allCovering.putAll(
Create a build error or a run error? It shouldn't have a build error.
Sean
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Tuesday, November 21, 2017 5:26 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hello Sean,
Thank you very much for the help, finally I am able to generate the Html
output file with tlink statement using piper file.
Although I have taken latest trunk update, in LabValuFinder.java the
putAll() method giving build error. this was the culprit. for me to get it
worked, I have commented the code and run it.
@SuppressWarnings( { "rawtypes", "unchecked" } ) // hold my beer and watch
this...
static private Map<Annotation, List<IdentifiedAnnotation>>
createCoveringMap( final JCas jCas,
final List<Class<? extends Annotation>> coveredClasses,
final List<Class<? extends IdentifiedAnnotation>> coveringClasses ) {
final Map<Annotation, List<IdentifiedAnnotation>> allCovering = new
HashMap<>();
// for ( Class covered : coveredClasses ) {
// for ( Class covering : coveringClasses ) {
// allCovering.putAll( JCasUtil.indexCovering( jCas, covered,
covering ) );
// }
// }
return allCovering;
}
I think this needs to be fixed, not sure though.
I have few more quires I will write it in separate thread.
On 20 November 2017 at 20:09, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> I have no idea why that isn't working. Ctakes-examples should have
> everything in its classpath.
>
> Ok, try this instead:
>
> Update to the latest version of trunk.
>
> On the left or right you may see a "maven projects" tab. If you don’t you
> can activate it using the menubar: View > Tool Windows > Maven Projects.
>
> Expand the "Maven Projects" tab. You should see a list or tree with
> "profiles" at the top, followed by "Apache cTAKES" and then ctakes modules.
>
> Expand "profiles" and click the box next to runPiperGui. If you don't see
> "runPiperGui" then you don't really have the latest version of trunk.
>
> Expand "Apache ctakes" and double-click clean. When Clean has finished
> double-click "compile". You should see ctakes compile for a while and
> then a gui should pop up. This is the Piper File Submitter. Follow the
> instructions on the wiki, pointing to your piper file, etc.
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=p8r3qe3ZhAJ2sfB9BKxtO6xgHUdUk0WWaB2A57OEJLs&s=pRJ81R6rCn_PT5H7O4cV9lSE4CMegjcRUNKIPNkqZZo&e=
> Piper+File+Submitter+GUI
>
> Sean
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Monday, November 20, 2017 7:12 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> I have installed intellij IDE imported maven project and compiled it using
> cTAKES+4.0+Developer+Install+Guide.
>
> Then I have followed the steps you have given for running the piper file
> using IDE
>
> I set the following in Run Configuration
>
> Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
> VM Options: -Xmx3G
> Working Directory: path/to/your/ctakes/
> Use Classpath of module: ctakes-examples
>
> Arguments:
> -p Path/to/your/PiperFile.piper
> --user yourUmlUsername
> --pass yourUmlsPassword
>
> But I am getting this error : Could not find or load main class
> org.apache.ctakes.core.pipeline.PiperFileRunner
> Could you please provide some inputs on it.
>
> On 17 November 2017 at 22:04, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Bhagwat,
> >
> > It is a little late, but I just checked in a maven profile that will
> start
> > the piper file submitter gui. To use it:
> >
> > 1. update your local sandbox with trunk
> > 2. There should be a maven tab somewhere in eclipse ...
> > 3. On the maven tab, enable the profile "runPiperGui"
> > 4. run maven compile
> >
> > The compilation stage should start, and near the end the piper gui will
> > pop up.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Friday, November 17, 2017 1:29 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hi Sean,
> >
> > I am using Eclipse Mars IDE.
> > Could you please tell me how to to set up an ide to run directly using
> the
> > source code.
> >
> > On 16 November 2017 at 20:23, Finan, Sean <Sean.Finan@childrens.harvard.
> > edu>
> > wrote:
> >
> > > Hi Bhagwat,
> > >
> > > I think that you are close, but that workflow won't pan out.
> > >
> > > If you want to run just like the ctakes release, run maven package,
> > > then go to the target/ directory in -distribution and unzip one of the
> > > created -bin files to another directory and then use that directory
> > > just like you would the ctakes release. Please note that you will
> > > need to copy the ctakes dictionary from your source into that
> > installation.
> > >
> > > If you are familiar with running from source that would be much easier.
> > > Are you using an IDE? It is very easy to set up an ide to run
> > > directly using the source code, which means that you don't have to
> > > both with the long package and copy process.
> > >
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > Sent: Thursday, November 16, 2017 4:17 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > > [SUSPICIOUS] [SUSPICIOUS]
> > >
> > > Hello Sean,
> > >
> > > Sorry to say but I haven't received any files, hope you are sending it
> > > on my personal email.
> > > Will it be possible to share it through dropbox or google drive?
> > >
> > > I have followed the steps provided on the link.
> > > After building ctakes-trunk, I have tried to run the piper file using
> > > ctake-distribution module where runpiper.bat file present, it means my
> > > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
> > >
> > > I ran the command
> > >
> > > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> > > D:\DefaultFastPipeline.piper --user USER --pass PASS
> > >
> > > it is giving following error:
> > >
> > > Error: Could not find or load main class org.apache.ctakes.core.
> > > pipeline.PiperFileRunner
> > >
> > > On 15 November 2017 at 22:07, Finan, Sean
> <Sean.Finan@childrens.harvard.
> > > edu>
> > > wrote:
> > >
> > > > I just sent it 2 more times ...
> > > >
> > > > -----Original Message-----
> > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > > Sent: Wednesday, November 15, 2017 11:20 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > > > [SUSPICIOUS] [SUSPICIOUS]
> > > >
> > > > Hi Sean,
> > > >
> > > > Unfortunately I haven't received it in spam folder too.
> > > >
> > > > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > > > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > > > or
> > > > > g_
> > > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > > > JZ
> > > > > MS
> > > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > > > rN
> > > > > wY
> > > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > > > m0
> > > > > O1
> > > > > 1vwvOMhuk&e=
> > > > > cTAKES+4.0+Developer+Install+Guide
> > > > >
> > > > > After that just run your piper as you have been.
> > > > >
> > > > > Sean
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > > > _m
> > > > > > > od
> > > > > > > el.j
> > > > > > > ar-
> > > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > px eF U&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
> > > > > > > .j
> > > > > > > av
> > > > > > > a-
> > > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > > > >
> > > > > > >
> > > > > > > and recompile, and it should remove the error.
> > > > > > >
> > > > > > >
> > > > > > > Tim
> > > > > > >
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > > > bhagwat.posane@gmail.com>]
> > > > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.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.posane@gmail.com
> <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > > <mailto:
> > > > > > > Sean.Finan@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.posane@gmail.com
> > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > > > is
> > > > > > > > > gl
> > > > > > > > > obal
> > > > > > > > > .com
> > > > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > > > >an
> > > > > > > >@
> > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > > to
> > > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > > Gandhi.Natarajan@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__g
> > > > > > > > > > > it
> > > > > > > > > > > hu
> > > > > > > > > > > b.co
> > > > > > > > > > > m_
> > > > > > > > > > > he
> > > > > > > > > > > al
> > > > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > > > Dw
> > > > > > > > > > > IB
> > > > > > > > > > > aQ&c
> > > > > > > > > > > =q
> > > > > > > > > > > S4
> > > > > > > > > > > go
> > > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > > > yI
> > > > > > > > > > > is
> > > > > > > > > > > CYNY
> > > > > > > > > > > mQ
> > > > > > > > > > > CP
> > > > > > > > > > > 6r
> > > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > > > qn
> > > > > > > > > > > 6b OrBk &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__g
> > > > > > > > > > > it
> > > > > > > > > > > hu
> > > > > > > > > > > b.co
> > > > > > > > > > > m_
> > > > > > > > > > > &d
> > > > > > > > > > > =D
> > > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlG
> > > > > > > > > > > Zs
> > > > > > > > > > > tT
> > > > > > > > > > > py
> > > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > > > Of
> > > > > > > > > > > qj
> > > > > > > > > > > R05A
> > > > > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > > il
> > > > > > > > > > > to
> > > > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > > <mailto:
> > > > > > > Sean.Finan@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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > > > op
> > > > > > > > > > > > lM
> > > > > > > > > > > > 69zy
> > > > > > > > > > > > _3
> > > > > > > > > > > > xh
> > > > > > > > > > > > Kw
> > > > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > > > pK
> > > > > > > > > > > > Gd
> > > > > > > > > > > > 4f7d
> > > > > > > > > > > > 4g
> > > > > > > > > > > > Ta
> > > > > > > > > > > > o&
> > > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > > > 5x
> > > > > > > > > > > > 7X
> > > > > > > > > > > > XCD3
> > > > > > > > > > > > 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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > > op
> > > > > > > > > > > > px
> > > > > > > > > > > > eFU&
> > > > > > > > > > > > r=
> > > > > > > > > > > > fs
> > > > > > > > > > > > 67
> > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > dL
> > > > > > > > > > > > _T
> > > > > > > > > > > > aKVF
> > > > > > > > > > > > qO
> > > > > > > > > > > > nS
> > > > > > > > > > > > Of
> > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > lf
> > > > > > > > > > > > 24
> > > > > > > > > > > > gMo6 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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > > op
> > > > > > > > > > > > px
> > > > > > > > > > > > eFU&
> > > > > > > > > > > > r=
> > > > > > > > > > > > fs
> > > > > > > > > > > > 67
> > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > dL
> > > > > > > > > > > > _T
> > > > > > > > > > > > aKVF
> > > > > > > > > > > > qO
> > > > > > > > > > > > nS
> > > > > > > > > > > > Of
> > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > lf
> > > > > > > > > > > > 24
> > > > > > > > > > > > gMo6
> > > > > > > > > > > > Gh
> > > > > > > > > > > > Jw s& e=
> > > > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > > > T
> > > > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.e
> > > > > > > du
> > > > > > > >>]
> > > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > > ma
> > > > > > > > > > > > il
> > > > > > > > > > > > to:d
> > > > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<
> mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> > <mailto:
> > > > > bhagwat
> > > > > > .
> > > > > > > posane@gmail.com>>>
> > > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > > ma
> > > > > > > > > > > > il
> > > > > > > > > > > > to:d
> > > > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > > > T7
> > > > > > > > > > > > po
> > > > > > > > > > > > plM6
> > > > > > > > > > > > 9z
> > > > > > > > > > > > y_
> > > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > > > TK
> > > > > > > > > > > > -
> > > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > > > _
> > > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > > > ja
> > > > > > > > > > > > n@
> > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > > > >
> > > > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > > > >
> > > > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > > > A_
> > > > > > > > > > > > > _svn
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > > or
> > > > > > > > > > > > > g_
> > > > > > > > > > > > > re
> > > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > > > oC
> > > > > > > > > > > > > op
> > > > > > > > > > > > > pxeF
> > > > > > > > > > > > > U&
> > > > > > > > > > > > > r=
> > > > > > > > > > > > > He
> > > > > > > > > > > > > up
> > > > > > > > > > > > > -I
> > > > > > > > > > > > > bs
> > > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > > > x6
> > > > > > > > > > > > > 67
> > > > > > > > > > > > > 4h&m
> > > > > > > > > > > > > =E
> > > > > > > > > > > > > fs
> > > > > > > > > > > > > fu
> > > > > > > > > > > > > j3
> > > > > > > > > > > > > 7p
> > > > > > > > > > > > > WN
> > > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > > > 6i
> > > > > > > > > > > > > ya
> > > > > > > > > > > > > qEJz
> > > > > > > > > > > > > 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.posane@gmail.com
> > > > > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > > > To:
> > > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > > > ><ma...@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
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Thanks,
> > > Bhagwat Posane
> > >
> >
> >
> >
> > --
> > Thanks,
> > Bhagwat Posane
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hello Sean,
Thank you very much for the help, finally I am able to generate the Html
output file with tlink statement using piper file.
Although I have taken latest trunk update, in LabValuFinder.java the
putAll() method giving build error. this was the culprit. for me to get it
worked, I have commented the code and run it.
@SuppressWarnings( { "rawtypes", "unchecked" } ) // hold my beer and watch
this...
static private Map<Annotation, List<IdentifiedAnnotation>>
createCoveringMap( final JCas jCas,
final List<Class<? extends Annotation>> coveredClasses,
final List<Class<? extends IdentifiedAnnotation>> coveringClasses ) {
final Map<Annotation, List<IdentifiedAnnotation>> allCovering = new
HashMap<>();
// for ( Class covered : coveredClasses ) {
// for ( Class covering : coveringClasses ) {
// allCovering.putAll( JCasUtil.indexCovering( jCas, covered,
covering ) );
// }
// }
return allCovering;
}
I think this needs to be fixed, not sure though.
I have few more quires I will write it in separate thread.
On 20 November 2017 at 20:09, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> I have no idea why that isn't working. Ctakes-examples should have
> everything in its classpath.
>
> Ok, try this instead:
>
> Update to the latest version of trunk.
>
> On the left or right you may see a "maven projects" tab. If you don’t you
> can activate it using the menubar: View > Tool Windows > Maven Projects.
>
> Expand the "Maven Projects" tab. You should see a list or tree with
> "profiles" at the top, followed by "Apache cTAKES" and then ctakes modules.
>
> Expand "profiles" and click the box next to runPiperGui. If you don't see
> "runPiperGui" then you don't really have the latest version of trunk.
>
> Expand "Apache ctakes" and double-click clean. When Clean has finished
> double-click "compile". You should see ctakes compile for a while and
> then a gui should pop up. This is the Piper File Submitter. Follow the
> instructions on the wiki, pointing to your piper file, etc.
>
> https://cwiki.apache.org/confluence/display/CTAKES/
> Piper+File+Submitter+GUI
>
> Sean
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Monday, November 20, 2017 7:12 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> I have installed intellij IDE imported maven project and compiled it using
> cTAKES+4.0+Developer+Install+Guide.
>
> Then I have followed the steps you have given for running the piper file
> using IDE
>
> I set the following in Run Configuration
>
> Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
> VM Options: -Xmx3G
> Working Directory: path/to/your/ctakes/
> Use Classpath of module: ctakes-examples
>
> Arguments:
> -p Path/to/your/PiperFile.piper
> --user yourUmlUsername
> --pass yourUmlsPassword
>
> But I am getting this error : Could not find or load main class
> org.apache.ctakes.core.pipeline.PiperFileRunner
> Could you please provide some inputs on it.
>
> On 17 November 2017 at 22:04, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Bhagwat,
> >
> > It is a little late, but I just checked in a maven profile that will
> start
> > the piper file submitter gui. To use it:
> >
> > 1. update your local sandbox with trunk
> > 2. There should be a maven tab somewhere in eclipse ...
> > 3. On the maven tab, enable the profile "runPiperGui"
> > 4. run maven compile
> >
> > The compilation stage should start, and near the end the piper gui will
> > pop up.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Friday, November 17, 2017 1:29 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hi Sean,
> >
> > I am using Eclipse Mars IDE.
> > Could you please tell me how to to set up an ide to run directly using
> the
> > source code.
> >
> > On 16 November 2017 at 20:23, Finan, Sean <Sean.Finan@childrens.harvard.
> > edu>
> > wrote:
> >
> > > Hi Bhagwat,
> > >
> > > I think that you are close, but that workflow won't pan out.
> > >
> > > If you want to run just like the ctakes release, run maven package,
> > > then go to the target/ directory in -distribution and unzip one of the
> > > created -bin files to another directory and then use that directory
> > > just like you would the ctakes release. Please note that you will
> > > need to copy the ctakes dictionary from your source into that
> > installation.
> > >
> > > If you are familiar with running from source that would be much easier.
> > > Are you using an IDE? It is very easy to set up an ide to run
> > > directly using the source code, which means that you don't have to
> > > both with the long package and copy process.
> > >
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > Sent: Thursday, November 16, 2017 4:17 AM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > > [SUSPICIOUS] [SUSPICIOUS]
> > >
> > > Hello Sean,
> > >
> > > Sorry to say but I haven't received any files, hope you are sending it
> > > on my personal email.
> > > Will it be possible to share it through dropbox or google drive?
> > >
> > > I have followed the steps provided on the link.
> > > After building ctakes-trunk, I have tried to run the piper file using
> > > ctake-distribution module where runpiper.bat file present, it means my
> > > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
> > >
> > > I ran the command
> > >
> > > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> > > D:\DefaultFastPipeline.piper --user USER --pass PASS
> > >
> > > it is giving following error:
> > >
> > > Error: Could not find or load main class org.apache.ctakes.core.
> > > pipeline.PiperFileRunner
> > >
> > > On 15 November 2017 at 22:07, Finan, Sean
> <Sean.Finan@childrens.harvard.
> > > edu>
> > > wrote:
> > >
> > > > I just sent it 2 more times ...
> > > >
> > > > -----Original Message-----
> > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > > Sent: Wednesday, November 15, 2017 11:20 AM
> > > > To: dev@ctakes.apache.org
> > > > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > > > [SUSPICIOUS] [SUSPICIOUS]
> > > >
> > > > Hi Sean,
> > > >
> > > > Unfortunately I haven't received it in spam folder too.
> > > >
> > > > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > > > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > > > or
> > > > > g_
> > > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > > > JZ
> > > > > MS
> > > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > > > rN
> > > > > wY
> > > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > > > m0
> > > > > O1
> > > > > 1vwvOMhuk&e=
> > > > > cTAKES+4.0+Developer+Install+Guide
> > > > >
> > > > > After that just run your piper as you have been.
> > > > >
> > > > > Sean
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > > > _m
> > > > > > > od
> > > > > > > el.j
> > > > > > > ar-
> > > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > px eF U&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
> > > > > > > .j
> > > > > > > av
> > > > > > > a-
> > > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > > > >
> > > > > > >
> > > > > > > and recompile, and it should remove the error.
> > > > > > >
> > > > > > >
> > > > > > > Tim
> > > > > > >
> > > > > > >
> > > > > > > ________________________________
> > > > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > > > bhagwat.posane@gmail.com>]
> > > > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.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.posane@gmail.com
> <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > > <mailto:
> > > > > > > Sean.Finan@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.posane@gmail.com
> > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > > > is
> > > > > > > > > gl
> > > > > > > > > obal
> > > > > > > > > .com
> > > > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > > > >an
> > > > > > > >@
> > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > > to
> > > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > > Gandhi.Natarajan@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__g
> > > > > > > > > > > it
> > > > > > > > > > > hu
> > > > > > > > > > > b.co
> > > > > > > > > > > m_
> > > > > > > > > > > he
> > > > > > > > > > > al
> > > > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > > > Dw
> > > > > > > > > > > IB
> > > > > > > > > > > aQ&c
> > > > > > > > > > > =q
> > > > > > > > > > > S4
> > > > > > > > > > > go
> > > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > > > yI
> > > > > > > > > > > is
> > > > > > > > > > > CYNY
> > > > > > > > > > > mQ
> > > > > > > > > > > CP
> > > > > > > > > > > 6r
> > > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > > > qn
> > > > > > > > > > > 6b OrBk &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__g
> > > > > > > > > > > it
> > > > > > > > > > > hu
> > > > > > > > > > > b.co
> > > > > > > > > > > m_
> > > > > > > > > > > &d
> > > > > > > > > > > =D
> > > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlG
> > > > > > > > > > > Zs
> > > > > > > > > > > tT
> > > > > > > > > > > py
> > > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > > > Of
> > > > > > > > > > > qj
> > > > > > > > > > > R05A
> > > > > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > > il
> > > > > > > > > > > to
> > > > > > > > > > > :d
> > > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > > <mailto:
> > > > > > > Sean.Finan@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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > > > op
> > > > > > > > > > > > lM
> > > > > > > > > > > > 69zy
> > > > > > > > > > > > _3
> > > > > > > > > > > > xh
> > > > > > > > > > > > Kw
> > > > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > > > pK
> > > > > > > > > > > > Gd
> > > > > > > > > > > > 4f7d
> > > > > > > > > > > > 4g
> > > > > > > > > > > > Ta
> > > > > > > > > > > > o&
> > > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > > > 5x
> > > > > > > > > > > > 7X
> > > > > > > > > > > > XCD3
> > > > > > > > > > > > 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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > > op
> > > > > > > > > > > > px
> > > > > > > > > > > > eFU&
> > > > > > > > > > > > r=
> > > > > > > > > > > > fs
> > > > > > > > > > > > 67
> > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > dL
> > > > > > > > > > > > _T
> > > > > > > > > > > > aKVF
> > > > > > > > > > > > qO
> > > > > > > > > > > > nS
> > > > > > > > > > > > Of
> > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > lf
> > > > > > > > > > > > 24
> > > > > > > > > > > > gMo6 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_
> > > > > > > > > > > > _c
> > > > > > > > > > > > wiki
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > > op
> > > > > > > > > > > > px
> > > > > > > > > > > > eFU&
> > > > > > > > > > > > r=
> > > > > > > > > > > > fs
> > > > > > > > > > > > 67
> > > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > > dL
> > > > > > > > > > > > _T
> > > > > > > > > > > > aKVF
> > > > > > > > > > > > qO
> > > > > > > > > > > > nS
> > > > > > > > > > > > Of
> > > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > > lf
> > > > > > > > > > > > 24
> > > > > > > > > > > > gMo6
> > > > > > > > > > > > Gh
> > > > > > > > > > > > Jw s& e=
> > > > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > > > T
> > > > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > > > ar
> > > > > > > va
> > > > > > > rd.e
> > > > > > > du
> > > > > > > >>]
> > > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > > ma
> > > > > > > > > > > > il
> > > > > > > > > > > > to:d
> > > > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<
> mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> > <mailto:
> > > > > bhagwat
> > > > > > .
> > > > > > > posane@gmail.com>>>
> > > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > > ma
> > > > > > > > > > > > il
> > > > > > > > > > > > to:d
> > > > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > > > T7
> > > > > > > > > > > > po
> > > > > > > > > > > > plM6
> > > > > > > > > > > > 9z
> > > > > > > > > > > > y_
> > > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > > > TK
> > > > > > > > > > > > -
> > > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > > > _
> > > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > > > ja
> > > > > > > > > > > > n@
> > > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > > > >
> > > > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > > > >
> > > > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > > > A_
> > > > > > > > > > > > > _svn
> > > > .
> > > > > > > apache.
> > > > > > > > > > > > > or
> > > > > > > > > > > > > g_
> > > > > > > > > > > > > re
> > > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > > > oC
> > > > > > > > > > > > > op
> > > > > > > > > > > > > pxeF
> > > > > > > > > > > > > U&
> > > > > > > > > > > > > r=
> > > > > > > > > > > > > He
> > > > > > > > > > > > > up
> > > > > > > > > > > > > -I
> > > > > > > > > > > > > bs
> > > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > > > x6
> > > > > > > > > > > > > 67
> > > > > > > > > > > > > 4h&m
> > > > > > > > > > > > > =E
> > > > > > > > > > > > > fs
> > > > > > > > > > > > > fu
> > > > > > > > > > > > > j3
> > > > > > > > > > > > > 7p
> > > > > > > > > > > > > WN
> > > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > > > 6i
> > > > > > > > > > > > > ya
> > > > > > > > > > > > > qEJz
> > > > > > > > > > > > > 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.posane@gmail.com
> > > > > > <mailto:
> > > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > > to
> > > > > > > :b
> > > > > > > hagw
> > > > > > > a
> > > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > > > To:
> > > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > > > ><ma...@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
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Thanks,
> > > Bhagwat Posane
> > >
> >
> >
> >
> > --
> > Thanks,
> > Bhagwat Posane
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Bhagwat,
I have no idea why that isn't working. Ctakes-examples should have everything in its classpath.
Ok, try this instead:
Update to the latest version of trunk.
On the left or right you may see a "maven projects" tab. If you don’t you can activate it using the menubar: View > Tool Windows > Maven Projects.
Expand the "Maven Projects" tab. You should see a list or tree with "profiles" at the top, followed by "Apache cTAKES" and then ctakes modules.
Expand "profiles" and click the box next to runPiperGui. If you don't see "runPiperGui" then you don't really have the latest version of trunk.
Expand "Apache ctakes" and double-click clean. When Clean has finished double-click "compile". You should see ctakes compile for a while and then a gui should pop up. This is the Piper File Submitter. Follow the instructions on the wiki, pointing to your piper file, etc.
https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI
Sean
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Monday, November 20, 2017 7:12 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hello Sean,
I have installed intellij IDE imported maven project and compiled it using
cTAKES+4.0+Developer+Install+Guide.
Then I have followed the steps you have given for running the piper file
using IDE
I set the following in Run Configuration
Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
VM Options: -Xmx3G
Working Directory: path/to/your/ctakes/
Use Classpath of module: ctakes-examples
Arguments:
-p Path/to/your/PiperFile.piper
--user yourUmlUsername
--pass yourUmlsPassword
But I am getting this error : Could not find or load main class
org.apache.ctakes.core.pipeline.PiperFileRunner
Could you please provide some inputs on it.
On 17 November 2017 at 22:04, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> It is a little late, but I just checked in a maven profile that will start
> the piper file submitter gui. To use it:
>
> 1. update your local sandbox with trunk
> 2. There should be a maven tab somewhere in eclipse ...
> 3. On the maven tab, enable the profile "runPiperGui"
> 4. run maven compile
>
> The compilation stage should start, and near the end the piper gui will
> pop up.
>
> Sean
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Friday, November 17, 2017 1:29 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hi Sean,
>
> I am using Eclipse Mars IDE.
> Could you please tell me how to to set up an ide to run directly using the
> source code.
>
> On 16 November 2017 at 20:23, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Bhagwat,
> >
> > I think that you are close, but that workflow won't pan out.
> >
> > If you want to run just like the ctakes release, run maven package,
> > then go to the target/ directory in -distribution and unzip one of the
> > created -bin files to another directory and then use that directory
> > just like you would the ctakes release. Please note that you will
> > need to copy the ctakes dictionary from your source into that
> installation.
> >
> > If you are familiar with running from source that would be much easier.
> > Are you using an IDE? It is very easy to set up an ide to run
> > directly using the source code, which means that you don't have to
> > both with the long package and copy process.
> >
> >
> > Sean
> >
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Thursday, November 16, 2017 4:17 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hello Sean,
> >
> > Sorry to say but I haven't received any files, hope you are sending it
> > on my personal email.
> > Will it be possible to share it through dropbox or google drive?
> >
> > I have followed the steps provided on the link.
> > After building ctakes-trunk, I have tried to run the piper file using
> > ctake-distribution module where runpiper.bat file present, it means my
> > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
> >
> > I ran the command
> >
> > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> > D:\DefaultFastPipeline.piper --user USER --pass PASS
> >
> > it is giving following error:
> >
> > Error: Could not find or load main class org.apache.ctakes.core.
> > pipeline.PiperFileRunner
> >
> > On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard.
> > edu>
> > wrote:
> >
> > > I just sent it 2 more times ...
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > Sent: Wednesday, November 15, 2017 11:20 AM
> > > To: dev@ctakes.apache.org
> > > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > > [SUSPICIOUS] [SUSPICIOUS]
> > >
> > > Hi Sean,
> > >
> > > Unfortunately I haven't received it in spam folder too.
> > >
> > > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > > or
> > > > g_
> > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > > JZ
> > > > MS
> > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > > rN
> > > > wY
> > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > > m0
> > > > O1
> > > > 1vwvOMhuk&e=
> > > > cTAKES+4.0+Developer+Install+Guide
> > > >
> > > > After that just run your piper as you have been.
> > > >
> > > > Sean
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > > _m
> > > > > > od
> > > > > > el.j
> > > > > > ar-
> > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > px eF U&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
> > > > > > .j
> > > > > > av
> > > > > > a-
> > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > > >
> > > > > >
> > > > > > and recompile, and it should remove the error.
> > > > > >
> > > > > >
> > > > > > Tim
> > > > > >
> > > > > >
> > > > > > ________________________________
> > > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com>]
> > > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > <mailto:
> > > > > > Sean.Finan@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.posane@gmail.com
> <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > > is
> > > > > > > > gl
> > > > > > > > obal
> > > > > > > > .com
> > > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > > >an
> > > > > > >@
> > > > > > 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.posane@gmail.com
> > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > to
> > > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > Gandhi.Natarajan@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__g
> > > > > > > > > > it
> > > > > > > > > > hu
> > > > > > > > > > b.co
> > > > > > > > > > m_
> > > > > > > > > > he
> > > > > > > > > > al
> > > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > > Dw
> > > > > > > > > > IB
> > > > > > > > > > aQ&c
> > > > > > > > > > =q
> > > > > > > > > > S4
> > > > > > > > > > go
> > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > > yI
> > > > > > > > > > is
> > > > > > > > > > CYNY
> > > > > > > > > > mQ
> > > > > > > > > > CP
> > > > > > > > > > 6r
> > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > > qn
> > > > > > > > > > 6b OrBk &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__g
> > > > > > > > > > it
> > > > > > > > > > hu
> > > > > > > > > > b.co
> > > > > > > > > > m_
> > > > > > > > > > &d
> > > > > > > > > > =D
> > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlG
> > > > > > > > > > Zs
> > > > > > > > > > tT
> > > > > > > > > > py
> > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > > Of
> > > > > > > > > > qj
> > > > > > > > > > R05A
> > > > > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > il
> > > > > > > > > > to
> > > > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > <mailto:
> > > > > > Sean.Finan@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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > > op
> > > > > > > > > > > lM
> > > > > > > > > > > 69zy
> > > > > > > > > > > _3
> > > > > > > > > > > xh
> > > > > > > > > > > Kw
> > > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > > pK
> > > > > > > > > > > Gd
> > > > > > > > > > > 4f7d
> > > > > > > > > > > 4g
> > > > > > > > > > > Ta
> > > > > > > > > > > o&
> > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > > 5x
> > > > > > > > > > > 7X
> > > > > > > > > > > XCD3
> > > > > > > > > > > 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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > op
> > > > > > > > > > > px
> > > > > > > > > > > eFU&
> > > > > > > > > > > r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > dL
> > > > > > > > > > > _T
> > > > > > > > > > > aKVF
> > > > > > > > > > > qO
> > > > > > > > > > > nS
> > > > > > > > > > > Of
> > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > lf
> > > > > > > > > > > 24
> > > > > > > > > > > gMo6 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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > op
> > > > > > > > > > > px
> > > > > > > > > > > eFU&
> > > > > > > > > > > r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > dL
> > > > > > > > > > > _T
> > > > > > > > > > > aKVF
> > > > > > > > > > > qO
> > > > > > > > > > > nS
> > > > > > > > > > > Of
> > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > lf
> > > > > > > > > > > 24
> > > > > > > > > > > gMo6
> > > > > > > > > > > Gh
> > > > > > > > > > > Jw s& e=
> > > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > > T
> > > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.e
> > > > > > du
> > > > > > >>]
> > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > ma
> > > > > > > > > > > il
> > > > > > > > > > > to:d
> > > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mailto:
> > > > bhagwat
> > > > > .
> > > > > > posane@gmail.com>>>
> > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > ma
> > > > > > > > > > > il
> > > > > > > > > > > to:d
> > > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > > T7
> > > > > > > > > > > po
> > > > > > > > > > > plM6
> > > > > > > > > > > 9z
> > > > > > > > > > > y_
> > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > > TK
> > > > > > > > > > > -
> > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > > _
> > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > > ja
> > > > > > > > > > > n@
> > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > > >
> > > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > > A_
> > > > > > > > > > > > _svn
> > > .
> > > > > > apache.
> > > > > > > > > > > > or
> > > > > > > > > > > > g_
> > > > > > > > > > > > re
> > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > > oC
> > > > > > > > > > > > op
> > > > > > > > > > > > pxeF
> > > > > > > > > > > > U&
> > > > > > > > > > > > r=
> > > > > > > > > > > > He
> > > > > > > > > > > > up
> > > > > > > > > > > > -I
> > > > > > > > > > > > bs
> > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > > x6
> > > > > > > > > > > > 67
> > > > > > > > > > > > 4h&m
> > > > > > > > > > > > =E
> > > > > > > > > > > > fs
> > > > > > > > > > > > fu
> > > > > > > > > > > > j3
> > > > > > > > > > > > 7p
> > > > > > > > > > > > WN
> > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > > 6i
> > > > > > > > > > > > ya
> > > > > > > > > > > > qEJz
> > > > > > > > > > > > 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.posane@gmail.com
> > > > > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > > ><ma...@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
> > > >
> > >
> >
> >
> >
> > --
> > Thanks,
> > Bhagwat Posane
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hello Sean,
I have installed intellij IDE imported maven project and compiled it using
cTAKES+4.0+Developer+Install+Guide.
Then I have followed the steps you have given for running the piper file
using IDE
I set the following in Run Configuration
Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
VM Options: -Xmx3G
Working Directory: path/to/your/ctakes/
Use Classpath of module: ctakes-examples
Arguments:
-p Path/to/your/PiperFile.piper
--user yourUmlUsername
--pass yourUmlsPassword
But I am getting this error : Could not find or load main class
org.apache.ctakes.core.pipeline.PiperFileRunner
Could you please provide some inputs on it.
On 17 November 2017 at 22:04, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> It is a little late, but I just checked in a maven profile that will start
> the piper file submitter gui. To use it:
>
> 1. update your local sandbox with trunk
> 2. There should be a maven tab somewhere in eclipse ...
> 3. On the maven tab, enable the profile "runPiperGui"
> 4. run maven compile
>
> The compilation stage should start, and near the end the piper gui will
> pop up.
>
> Sean
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Friday, November 17, 2017 1:29 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hi Sean,
>
> I am using Eclipse Mars IDE.
> Could you please tell me how to to set up an ide to run directly using the
> source code.
>
> On 16 November 2017 at 20:23, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > Hi Bhagwat,
> >
> > I think that you are close, but that workflow won't pan out.
> >
> > If you want to run just like the ctakes release, run maven package,
> > then go to the target/ directory in -distribution and unzip one of the
> > created -bin files to another directory and then use that directory
> > just like you would the ctakes release. Please note that you will
> > need to copy the ctakes dictionary from your source into that
> installation.
> >
> > If you are familiar with running from source that would be much easier.
> > Are you using an IDE? It is very easy to set up an ide to run
> > directly using the source code, which means that you don't have to
> > both with the long package and copy process.
> >
> >
> > Sean
> >
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Thursday, November 16, 2017 4:17 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hello Sean,
> >
> > Sorry to say but I haven't received any files, hope you are sending it
> > on my personal email.
> > Will it be possible to share it through dropbox or google drive?
> >
> > I have followed the steps provided on the link.
> > After building ctakes-trunk, I have tried to run the piper file using
> > ctake-distribution module where runpiper.bat file present, it means my
> > CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
> >
> > I ran the command
> >
> > D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> > D:\DefaultFastPipeline.piper --user USER --pass PASS
> >
> > it is giving following error:
> >
> > Error: Could not find or load main class org.apache.ctakes.core.
> > pipeline.PiperFileRunner
> >
> > On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard.
> > edu>
> > wrote:
> >
> > > I just sent it 2 more times ...
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > > Sent: Wednesday, November 15, 2017 11:20 AM
> > > To: dev@ctakes.apache.org
> > > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > > [SUSPICIOUS] [SUSPICIOUS]
> > >
> > > Hi Sean,
> > >
> > > Unfortunately I haven't received it in spam folder too.
> > >
> > > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > > or
> > > > g_
> > > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > > JZ
> > > > MS
> > > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > > rN
> > > > wY
> > > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > > m0
> > > > O1
> > > > 1vwvOMhuk&e=
> > > > cTAKES+4.0+Developer+Install+Guide
> > > >
> > > > After that just run your piper as you have been.
> > > >
> > > > Sean
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > > _m
> > > > > > od
> > > > > > el.j
> > > > > > ar-
> > > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > px eF U&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
> > > > > > .j
> > > > > > av
> > > > > > a-
> > > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > > >
> > > > > >
> > > > > > and recompile, and it should remove the error.
> > > > > >
> > > > > >
> > > > > > Tim
> > > > > >
> > > > > >
> > > > > > ________________________________
> > > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com>]
> > > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > <mailto:
> > > > > > Sean.Finan@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.posane@gmail.com
> <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > > is
> > > > > > > > gl
> > > > > > > > obal
> > > > > > > > .com
> > > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > > >an
> > > > > > >@
> > > > > > 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.posane@gmail.com
> > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > to
> > > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > Gandhi.Natarajan@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__g
> > > > > > > > > > it
> > > > > > > > > > hu
> > > > > > > > > > b.co
> > > > > > > > > > m_
> > > > > > > > > > he
> > > > > > > > > > al
> > > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > > Dw
> > > > > > > > > > IB
> > > > > > > > > > aQ&c
> > > > > > > > > > =q
> > > > > > > > > > S4
> > > > > > > > > > go
> > > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > > yI
> > > > > > > > > > is
> > > > > > > > > > CYNY
> > > > > > > > > > mQ
> > > > > > > > > > CP
> > > > > > > > > > 6r
> > > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > > qn
> > > > > > > > > > 6b OrBk &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__g
> > > > > > > > > > it
> > > > > > > > > > hu
> > > > > > > > > > b.co
> > > > > > > > > > m_
> > > > > > > > > > &d
> > > > > > > > > > =D
> > > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlG
> > > > > > > > > > Zs
> > > > > > > > > > tT
> > > > > > > > > > py
> > > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > > Of
> > > > > > > > > > qj
> > > > > > > > > > R05A
> > > > > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > il
> > > > > > > > > > to
> > > > > > > > > > :d
> > > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > > <mailto:
> > > > > > Sean.Finan@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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > > op
> > > > > > > > > > > lM
> > > > > > > > > > > 69zy
> > > > > > > > > > > _3
> > > > > > > > > > > xh
> > > > > > > > > > > Kw
> > > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > > pK
> > > > > > > > > > > Gd
> > > > > > > > > > > 4f7d
> > > > > > > > > > > 4g
> > > > > > > > > > > Ta
> > > > > > > > > > > o&
> > > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > > 5x
> > > > > > > > > > > 7X
> > > > > > > > > > > XCD3
> > > > > > > > > > > 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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > op
> > > > > > > > > > > px
> > > > > > > > > > > eFU&
> > > > > > > > > > > r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > dL
> > > > > > > > > > > _T
> > > > > > > > > > > aKVF
> > > > > > > > > > > qO
> > > > > > > > > > > nS
> > > > > > > > > > > Of
> > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > lf
> > > > > > > > > > > 24
> > > > > > > > > > > gMo6 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_
> > > > > > > > > > > _c
> > > > > > > > > > > wiki
> > > .
> > > > > > apache.
> > > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > > op
> > > > > > > > > > > px
> > > > > > > > > > > eFU&
> > > > > > > > > > > r=
> > > > > > > > > > > fs
> > > > > > > > > > > 67
> > > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > > dL
> > > > > > > > > > > _T
> > > > > > > > > > > aKVF
> > > > > > > > > > > qO
> > > > > > > > > > > nS
> > > > > > > > > > > Of
> > > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > > lf
> > > > > > > > > > > 24
> > > > > > > > > > > gMo6
> > > > > > > > > > > Gh
> > > > > > > > > > > Jw s& e=
> > > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > > T
> > > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > > ar
> > > > > > va
> > > > > > rd.e
> > > > > > du
> > > > > > >>]
> > > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > ma
> > > > > > > > > > > il
> > > > > > > > > > > to:d
> > > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com
> <mailto:
> > > > bhagwat
> > > > > .
> > > > > > posane@gmail.com>>>
> > > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > > ma
> > > > > > > > > > > il
> > > > > > > > > > > to:d
> > > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > > T7
> > > > > > > > > > > po
> > > > > > > > > > > plM6
> > > > > > > > > > > 9z
> > > > > > > > > > > y_
> > > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > > TK
> > > > > > > > > > > -
> > > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > > _
> > > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > > ja
> > > > > > > > > > > n@
> > > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > > >
> > > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > > A_
> > > > > > > > > > > > _svn
> > > .
> > > > > > apache.
> > > > > > > > > > > > or
> > > > > > > > > > > > g_
> > > > > > > > > > > > re
> > > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > > oC
> > > > > > > > > > > > op
> > > > > > > > > > > > pxeF
> > > > > > > > > > > > U&
> > > > > > > > > > > > r=
> > > > > > > > > > > > He
> > > > > > > > > > > > up
> > > > > > > > > > > > -I
> > > > > > > > > > > > bs
> > > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > > x6
> > > > > > > > > > > > 67
> > > > > > > > > > > > 4h&m
> > > > > > > > > > > > =E
> > > > > > > > > > > > fs
> > > > > > > > > > > > fu
> > > > > > > > > > > > j3
> > > > > > > > > > > > 7p
> > > > > > > > > > > > WN
> > > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > > 6i
> > > > > > > > > > > > ya
> > > > > > > > > > > > qEJz
> > > > > > > > > > > > 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.posane@gmail.com
> > > > > <mailto:
> > > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > > to
> > > > > > :b
> > > > > > hagw
> > > > > > a
> > > > > > t.posane@gmail.com>>]
> > > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > > To:
> > > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > > ><ma...@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
> > > >
> > >
> >
> >
> >
> > --
> > Thanks,
> > Bhagwat Posane
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Bhagwat,
It is a little late, but I just checked in a maven profile that will start the piper file submitter gui. To use it:
1. update your local sandbox with trunk
2. There should be a maven tab somewhere in eclipse ...
3. On the maven tab, enable the profile "runPiperGui"
4. run maven compile
The compilation stage should start, and near the end the piper gui will pop up.
Sean
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Friday, November 17, 2017 1:29 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean,
I am using Eclipse Mars IDE.
Could you please tell me how to to set up an ide to run directly using the source code.
On 16 November 2017 at 20:23, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> I think that you are close, but that workflow won't pan out.
>
> If you want to run just like the ctakes release, run maven package,
> then go to the target/ directory in -distribution and unzip one of the
> created -bin files to another directory and then use that directory
> just like you would the ctakes release. Please note that you will
> need to copy the ctakes dictionary from your source into that installation.
>
> If you are familiar with running from source that would be much easier.
> Are you using an IDE? It is very easy to set up an ide to run
> directly using the source code, which means that you don't have to
> both with the long package and copy process.
>
>
> Sean
>
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Thursday, November 16, 2017 4:17 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> Sorry to say but I haven't received any files, hope you are sending it
> on my personal email.
> Will it be possible to share it through dropbox or google drive?
>
> I have followed the steps provided on the link.
> After building ctakes-trunk, I have tried to run the piper file using
> ctake-distribution module where runpiper.bat file present, it means my
> CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
>
> I ran the command
>
> D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> D:\DefaultFastPipeline.piper --user USER --pass PASS
>
> it is giving following error:
>
> Error: Could not find or load main class org.apache.ctakes.core.
> pipeline.PiperFileRunner
>
> On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > I just sent it 2 more times ...
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Wednesday, November 15, 2017 11:20 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hi Sean,
> >
> > Unfortunately I haven't received it in spam folder too.
> >
> > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > or
> > > g_
> > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > JZ
> > > MS
> > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > rN
> > > wY
> > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > m0
> > > O1
> > > 1vwvOMhuk&e=
> > > cTAKES+4.0+Developer+Install+Guide
> > >
> > > After that just run your piper as you have been.
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > _m
> > > > > od
> > > > > el.j
> > > > > ar-
> > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > px eF U&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
> > > > > .j
> > > > > av
> > > > > a-
> > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > >
> > > > >
> > > > > and recompile, and it should remove the error.
> > > > >
> > > > >
> > > > > Tim
> > > > >
> > > > >
> > > > > ________________________________
> > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com>]
> > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > To:
> > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > is
> > > > > > > gl
> > > > > > > obal
> > > > > > > .com
> > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > >an
> > > > > >@
> > > > > 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.posane@gmail.com
> <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > to
> > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@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__g
> > > > > > > > > it
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > he
> > > > > > > > > al
> > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > Dw
> > > > > > > > > IB
> > > > > > > > > aQ&c
> > > > > > > > > =q
> > > > > > > > > S4
> > > > > > > > > go
> > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > yI
> > > > > > > > > is
> > > > > > > > > CYNY
> > > > > > > > > mQ
> > > > > > > > > CP
> > > > > > > > > 6r
> > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > qn
> > > > > > > > > 6b OrBk &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__g
> > > > > > > > > it
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > &d
> > > > > > > > > =D
> > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlG
> > > > > > > > > Zs
> > > > > > > > > tT
> > > > > > > > > py
> > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > Of
> > > > > > > > > qj
> > > > > > > > > R05A
> > > > > > > > > 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.posane@gmail.com
> > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > il
> > > > > > > > > to
> > > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > op
> > > > > > > > > > lM
> > > > > > > > > > 69zy
> > > > > > > > > > _3
> > > > > > > > > > xh
> > > > > > > > > > Kw
> > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > pK
> > > > > > > > > > Gd
> > > > > > > > > > 4f7d
> > > > > > > > > > 4g
> > > > > > > > > > Ta
> > > > > > > > > > o&
> > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > 5x
> > > > > > > > > > 7X
> > > > > > > > > > XCD3
> > > > > > > > > > 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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > op
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > dL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > lf
> > > > > > > > > > 24
> > > > > > > > > > gMo6 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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > op
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > dL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > lf
> > > > > > > > > > 24
> > > > > > > > > > gMo6
> > > > > > > > > > Gh
> > > > > > > > > > Jw s& e=
> > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > T
> > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.e
> > > > > du
> > > > > >>]
> > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> > > bhagwat
> > > > .
> > > > > posane@gmail.com>>>
> > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > T7
> > > > > > > > > > po
> > > > > > > > > > plM6
> > > > > > > > > > 9z
> > > > > > > > > > y_
> > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > TK
> > > > > > > > > > -
> > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > _
> > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > ja
> > > > > > > > > > n@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > >
> > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > A_
> > > > > > > > > > > _svn
> > .
> > > > > apache.
> > > > > > > > > > > or
> > > > > > > > > > > g_
> > > > > > > > > > > re
> > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > oC
> > > > > > > > > > > op
> > > > > > > > > > > pxeF
> > > > > > > > > > > U&
> > > > > > > > > > > r=
> > > > > > > > > > > He
> > > > > > > > > > > up
> > > > > > > > > > > -I
> > > > > > > > > > > bs
> > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > x6
> > > > > > > > > > > 67
> > > > > > > > > > > 4h&m
> > > > > > > > > > > =E
> > > > > > > > > > > fs
> > > > > > > > > > > fu
> > > > > > > > > > > j3
> > > > > > > > > > > 7p
> > > > > > > > > > > WN
> > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > 6i
> > > > > > > > > > > ya
> > > > > > > > > > > qEJz
> > > > > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > ><ma...@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
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> > > > > > > > > > > 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
> > >
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Bhagwat,
Hopefully somebody familiar with Eclipse can better answer your question. I use IntelliJ, so some details are going to be different.
There should be a "run" menu item or button somewhere. That should be connected to some kind of "run configuration/setup" screen.
You should be able to set the following:
Main class : org.apache.ctakes.core.pipeline.PiperFileRunner
VM Options: -Xmx3G
Working Directory: path/to/your/ctakes/
Use Classpath of module: ctakes-examples
Arguments: (what follows is one line or arguments)
-p
Path/to/your/PiperFile.piper
-i
Path/to/your/input/dir/
-o
Path/to/your/output/dir/
-l
org/apache/ctakes/dictionary/lookup/fast/sno_rx_new.xml
--user
yourUmlUsername
--pass
yourUmlsPassword
Optionally, if you are running with trunk then you can launch a gui and use it to specify all of those arguments:
Main Class : org.apache.ctakes.gui.pipeline.PiperRunnerGui
VM Options: -Xmx3G
Working Directory: path/to/your/ctakes/
Use ClassPath of module: ctakes-gui
https://cwiki.apache.org/confluence/display/CTAKES/Piper+File+Submitter+GUI
Sean
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Friday, November 17, 2017 1:29 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean,
I am using Eclipse Mars IDE.
Could you please tell me how to to set up an ide to run directly using the source code.
On 16 November 2017 at 20:23, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> I think that you are close, but that workflow won't pan out.
>
> If you want to run just like the ctakes release, run maven package,
> then go to the target/ directory in -distribution and unzip one of the
> created -bin files to another directory and then use that directory
> just like you would the ctakes release. Please note that you will
> need to copy the ctakes dictionary from your source into that installation.
>
> If you are familiar with running from source that would be much easier.
> Are you using an IDE? It is very easy to set up an ide to run
> directly using the source code, which means that you don't have to
> both with the long package and copy process.
>
>
> Sean
>
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Thursday, November 16, 2017 4:17 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> Sorry to say but I haven't received any files, hope you are sending it
> on my personal email.
> Will it be possible to share it through dropbox or google drive?
>
> I have followed the steps provided on the link.
> After building ctakes-trunk, I have tried to run the piper file using
> ctake-distribution module where runpiper.bat file present, it means my
> CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
>
> I ran the command
>
> D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> D:\DefaultFastPipeline.piper --user USER --pass PASS
>
> it is giving following error:
>
> Error: Could not find or load main class org.apache.ctakes.core.
> pipeline.PiperFileRunner
>
> On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > I just sent it 2 more times ...
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Wednesday, November 15, 2017 11:20 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hi Sean,
> >
> > Unfortunately I haven't received it in spam folder too.
> >
> > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.
> > > or
> > > g_
> > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > > JZ
> > > MS
> > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIX
> > > rN
> > > wY
> > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHr
> > > m0
> > > O1
> > > 1vwvOMhuk&e=
> > > cTAKES+4.0+Developer+Install+Guide
> > >
> > > After that just run your piper as you have been.
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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
> > > > > _m
> > > > > od
> > > > > el.j
> > > > > ar-
> > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > px eF U&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
> > > > > .j
> > > > > av
> > > > > a-
> > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdio
> > > > > Co pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > >
> > > > >
> > > > > and recompile, and it should remove the error.
> > > > >
> > > > >
> > > > > Tim
> > > > >
> > > > >
> > > > > ________________________________
> > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com>]
> > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > To:
> > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@ar
> > > > > > > is
> > > > > > > gl
> > > > > > > obal
> > > > > > > .com
> > > > > ><mailto:Gandhi.Natarajan@arisglobal.com<mailto:Gandhi.Nataraj
> > > > > >an
> > > > > >@
> > > > > 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.posane@gmail.com
> <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > to
> > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@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__g
> > > > > > > > > it
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > he
> > > > > > > > > al
> > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=
> > > > > > > > > Dw
> > > > > > > > > IB
> > > > > > > > > aQ&c
> > > > > > > > > =q
> > > > > > > > > S4
> > > > > > > > > go
> > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > > > > > > > > yI
> > > > > > > > > is
> > > > > > > > > CYNY
> > > > > > > > > mQ
> > > > > > > > > CP
> > > > > > > > > 6r
> > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnw
> > > > > > > > > qn
> > > > > > > > > 6b OrBk &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__g
> > > > > > > > > it
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > &d
> > > > > > > > > =D
> > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlG
> > > > > > > > > Zs
> > > > > > > > > tT
> > > > > > > > > py
> > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnS
> > > > > > > > > Of
> > > > > > > > > qj
> > > > > > > > > R05A
> > > > > > > > > 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.posane@gmail.com
> > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > il
> > > > > > > > > to
> > > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7p
> > > > > > > > > > op
> > > > > > > > > > lM
> > > > > > > > > > 69zy
> > > > > > > > > > _3
> > > > > > > > > > xh
> > > > > > > > > > Kw
> > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> > > > > > > > > > pK
> > > > > > > > > > Gd
> > > > > > > > > > 4f7d
> > > > > > > > > > 4g
> > > > > > > > > > Ta
> > > > > > > > > > o&
> > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz
> > > > > > > > > > 5x
> > > > > > > > > > 7X
> > > > > > > > > > XCD3
> > > > > > > > > > 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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > op
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > dL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > lf
> > > > > > > > > > 24
> > > > > > > > > > gMo6 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_
> > > > > > > > > > _c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioC
> > > > > > > > > > op
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriA
> > > > > > > > > > dL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hK
> > > > > > > > > > lf
> > > > > > > > > > 24
> > > > > > > > > > gMo6
> > > > > > > > > > Gh
> > > > > > > > > > Jw s& e=
> > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator
> > > > > > > > > > +G UI 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.Miller@childrens.harvard.edu<mailto:
> > > > > > > > > > T
> > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.h
> > > > > ar
> > > > > va
> > > > > rd.e
> > > > > du
> > > > > >>]
> > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> > > bhagwat
> > > > .
> > > > > posane@gmail.com>>>
> > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><
> > > > > > > > > > ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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=qS4goWB
> > > > > > > > > > T7
> > > > > > > > > > po
> > > > > > > > > > plM6
> > > > > > > > > > 9z
> > > > > > > > > > y_
> > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4G
> > > > > > > > > > TK
> > > > > > > > > > -
> > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR
> > > > > > > > > > _
> > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNB
> > > > > > > > > > TC EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natara
> > > > > > > > > > ja
> > > > > > > > > > n@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@arisglobal.com>>> wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Bhagwat,
> > > > > > > > > > >
> > > > > > > > > > > The source code of cTAKES is available under
> > > > > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3
> > > > > > > > > > > A_
> > > > > > > > > > > _svn
> > .
> > > > > apache.
> > > > > > > > > > > or
> > > > > > > > > > > g_
> > > > > > > > > > > re
> > > > > > > > > > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> > > > > > > > > > > oC
> > > > > > > > > > > op
> > > > > > > > > > > pxeF
> > > > > > > > > > > U&
> > > > > > > > > > > r=
> > > > > > > > > > > He
> > > > > > > > > > > up
> > > > > > > > > > > -I
> > > > > > > > > > > bs
> > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uY
> > > > > > > > > > > x6
> > > > > > > > > > > 67
> > > > > > > > > > > 4h&m
> > > > > > > > > > > =E
> > > > > > > > > > > fs
> > > > > > > > > > > fu
> > > > > > > > > > > j3
> > > > > > > > > > > 7p
> > > > > > > > > > > WN
> > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs
> > > > > > > > > > > 6i
> > > > > > > > > > > ya
> > > > > > > > > > > qEJz
> > > > > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mail
> > > > > to
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > ><ma...@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
> > >
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hi Sean,
I am using Eclipse Mars IDE.
Could you please tell me how to to set up an ide to run directly using the
source code.
On 16 November 2017 at 20:23, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> I think that you are close, but that workflow won't pan out.
>
> If you want to run just like the ctakes release, run maven package, then
> go to the target/ directory in -distribution and unzip one of the created
> -bin files to another directory and then use that directory just like you
> would the ctakes release. Please note that you will need to copy the
> ctakes dictionary from your source into that installation.
>
> If you are familiar with running from source that would be much easier.
> Are you using an IDE? It is very easy to set up an ide to run directly
> using the source code, which means that you don't have to both with the
> long package and copy process.
>
>
> Sean
>
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Thursday, November 16, 2017 4:17 AM
> To: dev@ctakes.apache.org
> Subject: Re: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hello Sean,
>
> Sorry to say but I haven't received any files, hope you are sending it on
> my personal email.
> Will it be possible to share it through dropbox or google drive?
>
> I have followed the steps provided on the link.
> After building ctakes-trunk, I have tried to run the piper file using
> ctake-distribution module where runpiper.bat file present, it means my
> CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
>
> I ran the command
>
> D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
> D:\DefaultFastPipeline.piper --user USER --pass PASS
>
> it is giving following error:
>
> Error: Could not find or load main class org.apache.ctakes.core.
> pipeline.PiperFileRunner
>
> On 15 November 2017 at 22:07, Finan, Sean <Sean.Finan@childrens.harvard.
> edu>
> wrote:
>
> > I just sent it 2 more times ...
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> > Sent: Wednesday, November 15, 2017 11:20 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> > [SUSPICIOUS] [SUSPICIOUS]
> >
> > Hi Sean,
> >
> > Unfortunately I haven't received it in spam folder too.
> >
> > On Nov 15, 2017 7:47 PM, "Finan, Sean"
> > <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> > > g_
> > > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
> > > MS
> > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIXrN
> > > wY
> > > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHrm0
> > > O1
> > > 1vwvOMhuk&e=
> > > cTAKES+4.0+Developer+Install+Guide
> > >
> > > After that just run your piper as you have been.
> > >
> > > Sean
> > >
> > >
> > > -----Original Message-----
> > > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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_m
> > > > > od
> > > > > el.j
> > > > > ar-
> > > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > > > > eF U&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.j
> > > > > av
> > > > > a-
> > > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo
> > > > > pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > > >
> > > > >
> > > > > and recompile, and it should remove the error.
> > > > >
> > > > >
> > > > > Tim
> > > > >
> > > > >
> > > > > ________________________________
> > > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com>]
> > > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.har
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > > <ma...@childrens.harvard.edu><mailto:
> > > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.har
> > > > > va
> > > > > rd.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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@aris
> > > > > > > gl
> > > > > > > obal
> > > > > > > .com
> > > > > ><mailto:Gandhi.Natarajan@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.posane@gmail.com
> <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@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__git
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > he
> > > > > > > > > al
> > > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=Dw
> > > > > > > > > IB
> > > > > > > > > aQ&c
> > > > > > > > > =q
> > > > > > > > > S4
> > > > > > > > > go
> > > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyI
> > > > > > > > > is
> > > > > > > > > CYNY
> > > > > > > > > mQ
> > > > > > > > > CP
> > > > > > > > > 6r
> > > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn
> > > > > > > > > 6b OrBk &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__git
> > > > > > > > > hu
> > > > > > > > > b.co
> > > > > > > > > m_
> > > > > > > > > &d
> > > > > > > > > =D
> > > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
> > > > > > > > > 67
> > > > > > > > > GvlG
> > > > > > > > > Zs
> > > > > > > > > tT
> > > > > > > > > py
> > > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > > > > > > > qj
> > > > > > > > > R05A
> > > > > > > > > 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.posane@gmail.com
> > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > to
> > > > > > > > > :d
> > > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> > <mailto:
> > > > > Sean.Finan@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__c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7pop
> > > > > > > > > > lM
> > > > > > > > > > 69zy
> > > > > > > > > > _3
> > > > > > > > > > xh
> > > > > > > > > > Kw
> > > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpK
> > > > > > > > > > Gd
> > > > > > > > > > 4f7d
> > > > > > > > > > 4g
> > > > > > > > > > Ta
> > > > > > > > > > o&
> > > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x
> > > > > > > > > > 7X
> > > > > > > > > > XCD3
> > > > > > > > > > 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__c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf
> > > > > > > > > > 24
> > > > > > > > > > gMo6 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__c
> > > > > > > > > > wiki
> > .
> > > > > apache.
> > > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > > > > px
> > > > > > > > > > eFU&
> > > > > > > > > > r=
> > > > > > > > > > fs
> > > > > > > > > > 67
> > > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL
> > > > > > > > > > _T
> > > > > > > > > > aKVF
> > > > > > > > > > qO
> > > > > > > > > > nS
> > > > > > > > > > Of
> > > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf
> > > > > > > > > > 24
> > > > > > > > > > gMo6
> > > > > > > > > > Gh
> > > > > > > > > > Jw s& e=
> > > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator+G
> > > > > > > > > > UI 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.Miller@childrens.harvard.edu<mailto:T
> > > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.har
> > > > > va
> > > > > rd.e
> > > > > du
> > > > > >>]
> > > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> > > bhagwat
> > > > .
> > > > > posane@gmail.com>>>
> > > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > > il
> > > > > > > > > > to:d
> > > > > ev@ctakes.apache.org<ma...@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=qS4goWBT7
> > > > > > > > > > po
> > > > > > > > > > plM6
> > > > > > > > > > 9z
> > > > > > > > > > y_
> > > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK
> > > > > > > > > > -
> > > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_
> > > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTC
> > > > > > > > > > EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Nataraja
> > > > > > > > > > n@
> > > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > > Gandhi.Natarajan@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_3xhKwEW14JZMSdioC
> > > > > > > > > > > op
> > > > > > > > > > > pxeF
> > > > > > > > > > > U&
> > > > > > > > > > > r=
> > > > > > > > > > > He
> > > > > > > > > > > up
> > > > > > > > > > > -I
> > > > > > > > > > > bs
> > > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6
> > > > > > > > > > > 67
> > > > > > > > > > > 4h&m
> > > > > > > > > > > =E
> > > > > > > > > > > fs
> > > > > > > > > > > fu
> > > > > > > > > > > j3
> > > > > > > > > > > 7p
> > > > > > > > > > > WN
> > > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6i
> > > > > > > > > > > ya
> > > > > > > > > > > qEJz
> > > > > > > > > > > 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.posane@gmail.com
> > > > <mailto:
> > > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > > :b
> > > > > hagw
> > > > > a
> > > > > t.posane@gmail.com>>]
> > > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > > To:
> > > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > > ><ma...@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
> > >
> >
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Bhagwat,
I think that you are close, but that workflow won't pan out.
If you want to run just like the ctakes release, run maven package, then go to the target/ directory in -distribution and unzip one of the created -bin files to another directory and then use that directory just like you would the ctakes release. Please note that you will need to copy the ctakes dictionary from your source into that installation.
If you are familiar with running from source that would be much easier. Are you using an IDE? It is very easy to set up an ide to run directly using the source code, which means that you don't have to both with the long package and copy process.
Sean
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Thursday, November 16, 2017 4:17 AM
To: dev@ctakes.apache.org
Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hello Sean,
Sorry to say but I haven't received any files, hope you are sending it on my personal email.
Will it be possible to share it through dropbox or google drive?
I have followed the steps provided on the link.
After building ctakes-trunk, I have tried to run the piper file using ctake-distribution module where runpiper.bat file present, it means my CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
I ran the command
D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p D:\DefaultFastPipeline.piper --user USER --pass PASS
it is giving following error:
Error: Could not find or load main class org.apache.ctakes.core.pipeline.PiperFileRunner
On 15 November 2017 at 22:07, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> I just sent it 2 more times ...
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Wednesday, November 15, 2017 11:20 AM
> To: dev@ctakes.apache.org
> Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hi Sean,
>
> Unfortunately I haven't received it in spam folder too.
>
> On Nov 15, 2017 7:47 PM, "Finan, Sean"
> <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> > g_
> > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
> > MS
> > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIXrN
> > wY
> > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHrm0
> > O1
> > 1vwvOMhuk&e=
> > cTAKES+4.0+Developer+Install+Guide
> >
> > After that just run your piper as you have been.
> >
> > Sean
> >
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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_m
> > > > od
> > > > el.j
> > > > ar-
> > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > > > eF U&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.j
> > > > av
> > > > a-
> > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo
> > > > pp xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > >
> > > >
> > > > and recompile, and it should remove the error.
> > > >
> > > >
> > > > Tim
> > > >
> > > >
> > > > ________________________________
> > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com>]
> > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.har
> > > > va
> > > > rd.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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > <ma...@childrens.harvard.edu><mailto:
> > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.har
> > > > va
> > > > rd.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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > To:
> > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> <mailto:
> > > > Sean.Finan@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@aris
> > > > > > gl
> > > > > > obal
> > > > > > .com
> > > > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > :d
> > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > Gandhi.Natarajan@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__git
> > > > > > > > hu
> > > > > > > > b.co
> > > > > > > > m_
> > > > > > > > he
> > > > > > > > al
> > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=Dw
> > > > > > > > IB
> > > > > > > > aQ&c
> > > > > > > > =q
> > > > > > > > S4
> > > > > > > > go
> > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyI
> > > > > > > > is
> > > > > > > > CYNY
> > > > > > > > mQ
> > > > > > > > CP
> > > > > > > > 6r
> > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn
> > > > > > > > 6b OrBk &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__git
> > > > > > > > hu
> > > > > > > > b.co
> > > > > > > > m_
> > > > > > > > &d
> > > > > > > > =D
> > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
> > > > > > > > 67
> > > > > > > > GvlG
> > > > > > > > Zs
> > > > > > > > tT
> > > > > > > > py
> > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > > > > > > qj
> > > > > > > > R05A
> > > > > > > > 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.posane@gmail.com
> <mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > to
> > > > > > > > :d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> <mailto:
> > > > Sean.Finan@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__c
> > > > > > > > > wiki
> .
> > > > apache.
> > > > > > > > > org_confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7pop
> > > > > > > > > lM
> > > > > > > > > 69zy
> > > > > > > > > _3
> > > > > > > > > xh
> > > > > > > > > Kw
> > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpK
> > > > > > > > > Gd
> > > > > > > > > 4f7d
> > > > > > > > > 4g
> > > > > > > > > Ta
> > > > > > > > > o&
> > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x
> > > > > > > > > 7X
> > > > > > > > > XCD3
> > > > > > > > > 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__c
> > > > > > > > > wiki
> .
> > > > apache.
> > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > > > px
> > > > > > > > > eFU&
> > > > > > > > > r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL
> > > > > > > > > _T
> > > > > > > > > aKVF
> > > > > > > > > qO
> > > > > > > > > nS
> > > > > > > > > Of
> > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf
> > > > > > > > > 24
> > > > > > > > > gMo6 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__c
> > > > > > > > > wiki
> .
> > > > apache.
> > > > > > > > > org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
> > > > > > > > > px
> > > > > > > > > eFU&
> > > > > > > > > r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL
> > > > > > > > > _T
> > > > > > > > > aKVF
> > > > > > > > > qO
> > > > > > > > > nS
> > > > > > > > > Of
> > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf
> > > > > > > > > 24
> > > > > > > > > gMo6
> > > > > > > > > Gh
> > > > > > > > > Jw s& e=
> > > > > > > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator+G
> > > > > > > > > UI 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.Miller@childrens.harvard.edu<mailto:T
> > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.har
> > > > va
> > > > rd.e
> > > > du
> > > > >>]
> > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > il
> > > > > > > > > to:d
> > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> > bhagwat
> > > .
> > > > posane@gmail.com>>>
> > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><ma
> > > > > > > > > il
> > > > > > > > > to:d
> > > > ev@ctakes.apache.org<ma...@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=qS4goWBT7
> > > > > > > > > po
> > > > > > > > > plM6
> > > > > > > > > 9z
> > > > > > > > > y_
> > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK
> > > > > > > > > -
> > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_
> > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTC
> > > > > > > > > EN aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Nataraja
> > > > > > > > > n@
> > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > Gandhi.Natarajan@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_3xhKwEW14JZMSdioC
> > > > > > > > > > op
> > > > > > > > > > pxeF
> > > > > > > > > > U&
> > > > > > > > > > r=
> > > > > > > > > > He
> > > > > > > > > > up
> > > > > > > > > > -I
> > > > > > > > > > bs
> > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6
> > > > > > > > > > 67
> > > > > > > > > > 4h&m
> > > > > > > > > > =E
> > > > > > > > > > fs
> > > > > > > > > > fu
> > > > > > > > > > j3
> > > > > > > > > > 7p
> > > > > > > > > > WN
> > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6i
> > > > > > > > > > ya
> > > > > > > > > > qEJz
> > > > > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto
> > > > :b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > To:
> > > > > > > > > > dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > ><ma...@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
> >
>
--
Thanks,
Bhagwat Posane
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hello Sean,
Sorry to say but I haven't received any files, hope you are sending it on
my personal email.
Will it be possible to share it through dropbox or google drive?
I have followed the steps provided on the link.
After building ctakes-trunk, I have tried to run the piper file using
ctake-distribution module where runpiper.bat file present, it means my
CTAKES_HOME will be (\cTakes_trunk\ctakes-distribution\src\main).
I ran the command
D:\cTakes\ctakes-distribution\src\main>bin\runPiperFile.bat -p
D:\DefaultFastPipeline.piper --user USER --pass PASS
it is giving following error:
Error: Could not find or load main class
org.apache.ctakes.core.pipeline.PiperFileRunner
On 15 November 2017 at 22:07, Finan, Sean <Se...@childrens.harvard.edu>
wrote:
> I just sent it 2 more times ...
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
> Sent: Wednesday, November 15, 2017 11:20 AM
> To: dev@ctakes.apache.org
> Subject: RE: source code of user installation of cTakes. [EXTERNAL]
> [SUSPICIOUS] [SUSPICIOUS]
>
> Hi Sean,
>
> Unfortunately I haven't received it in spam folder too.
>
> On Nov 15, 2017 7:47 PM, "Finan, Sean" <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIXrNwY
> > cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHrm0O1
> > 1vwvOMhuk&e=
> > cTAKES+4.0+Developer+Install+Guide
> >
> > After that just run your piper as you have been.
> >
> > Sean
> >
> >
> > -----Original Message-----
> > From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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_mod
> > > > el.j
> > > > ar-
> > > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeF
> > > > U&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.jav
> > > > a-
> > > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCopp
> > > > xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > > >
> > > >
> > > > and recompile, and it should remove the error.
> > > >
> > > >
> > > > Tim
> > > >
> > > >
> > > > ________________________________
> > > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com>]
> > > > Sent: Monday, November 13, 2017 3:25 AM
> > > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harva
> > > > rd.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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > Sent: Friday, November 10, 2017 6:13 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > > <ma...@childrens.harvard.edu><mailto:
> > > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harva
> > > > rd.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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> <mailto:
> > > > Sean.Finan@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisgl
> > > > > > obal
> > > > > > .com
> > > > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > Gandhi.Natarajan@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__githu
> > > > > > > > b.co
> > > > > > > > m_
> > > > > > > > he
> > > > > > > > al
> > > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIB
> > > > > > > > aQ&c
> > > > > > > > =q
> > > > > > > > S4
> > > > > > > > go
> > > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIis
> > > > > > > > CYNY
> > > > > > > > mQ
> > > > > > > > CP
> > > > > > > > 6r
> > > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6b
> > > > > > > > OrBk &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__githu
> > > > > > > > b.co
> > > > > > > > m_
> > > > > > > > &d
> > > > > > > > =D
> > > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67
> > > > > > > > GvlG
> > > > > > > > Zs
> > > > > > > > tT
> > > > > > > > py
> > > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqj
> > > > > > > > R05A
> > > > > > > > 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.posane@gmail.com
> <mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > > :d
> > > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu
> <mailto:
> > > > Sean.Finan@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=qS4goWBT7poplM
> > > > > > > > > 69zy
> > > > > > > > > _3
> > > > > > > > > xh
> > > > > > > > > Kw
> > > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd
> > > > > > > > > 4f7d
> > > > > > > > > 4g
> > > > > > > > > Ta
> > > > > > > > > o&
> > > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7X
> > > > > > > > > XCD3
> > > > > > > > > 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_3xhKwEW14JZMSdioCoppx
> > > > > > > > > eFU&
> > > > > > > > > r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_T
> > > > > > > > > aKVF
> > > > > > > > > qO
> > > > > > > > > nS
> > > > > > > > > Of
> > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24
> > > > > > > > > gMo6 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_3xhKwEW14JZMSdioCoppx
> > > > > > > > > eFU&
> > > > > > > > > r=
> > > > > > > > > fs
> > > > > > > > > 67
> > > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_T
> > > > > > > > > aKVF
> > > > > > > > > qO
> > > > > > > > > nS
> > > > > > > > > Of
> > > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24
> > > > > > > > > gMo6
> > > > > > > > > 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.Miller@childrens.harvard.edu<mailto:T
> > > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harva
> > > > rd.e
> > > > du
> > > > >>]
> > > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > to:d
> > > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> > bhagwat
> > > .
> > > > posane@gmail.com>>>
> > > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > > To:
> > > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > > to:d
> > > > ev@ctakes.apache.org<ma...@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=qS4goWBT7po
> > > > > > > > > plM6
> > > > > > > > > 9z
> > > > > > > > > y_
> > > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_
> > > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCEN
> > > > > > > > > aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > > Gandhi.Natarajan@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_3xhKwEW14JZMSdioCop
> > > > > > > > > > pxeF
> > > > > > > > > > U&
> > > > > > > > > > r=
> > > > > > > > > > He
> > > > > > > > > > up
> > > > > > > > > > -I
> > > > > > > > > > bs
> > > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx667
> > > > > > > > > > 4h&m
> > > > > > > > > > =E
> > > > > > > > > > fs
> > > > > > > > > > fu
> > > > > > > > > > j3
> > > > > > > > > > 7p
> > > > > > > > > > WN
> > > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iya
> > > > > > > > > > qEJz
> > > > > > > > > > 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.posane@gmail.com
> > > <mailto:
> > > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > > hagw
> > > > a
> > > > t.posane@gmail.com>>]
> > > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > > ><ma...@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
> >
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
I just sent it 2 more times ...
-----Original Message-----
From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
Sent: Wednesday, November 15, 2017 11:20 AM
To: dev@ctakes.apache.org
Subject: RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean,
Unfortunately I haven't received it in spam folder too.
On Nov 15, 2017 7:47 PM, "Finan, Sean" <Se...@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=JsLzIXrNwY
> cjOklz3XujyeiXMkufkblxy_PkPYr23DY&s=70Yd1blUCxM6w8yscAYAN8p66nCVHrm0O1
> 1vwvOMhuk&e=
> cTAKES+4.0+Developer+Install+Guide
>
> After that just run your piper as you have been.
>
> Sean
>
>
> -----Original Message-----
> From: Bhagwat Posane [mailto:bhagwat.posane@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.posane@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.Miller@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_mod
> > > el.j
> > > ar-
> > > 3Fview-3Dlog&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeF
> > > U&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.jav
> > > a-
> > > 3Fview-3Dmarkup&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCopp
> > > xeFU &r= fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > sKTgd6XX8SzXUjskO039AoLyPc5Bkd30KO2tnioosh0&s=
> > > EDaptVRyDuEbjBXQ4F4I4fjxR5qHaPebxKn6smA92fU&e=
> > >
> > >
> > > and recompile, and it should remove the error.
> > >
> > >
> > > Tim
> > >
> > >
> > > ________________________________
> > > From: Bhagwat Posane <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com>]
> > > Sent: Monday, November 13, 2017 3:25 AM
> > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harva
> > > rd.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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > Sent: Friday, November 10, 2017 6:13 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > <ma...@childrens.harvard.edu><mailto:
> > > Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@childrens.harva
> > > rd.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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > > Sean.Finan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > To:
> > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisgl
> > > > > obal
> > > > > .com
> > > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > Gandhi.Natarajan@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__githu
> > > > > > > b.co
> > > > > > > m_
> > > > > > > he
> > > > > > > al
> > > > > > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIB
> > > > > > > aQ&c
> > > > > > > =q
> > > > > > > S4
> > > > > > > go
> > > > > > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIis
> > > > > > > CYNY
> > > > > > > mQ
> > > > > > > CP
> > > > > > > 6r
> > > > > > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6b
> > > > > > > OrBk &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__githu
> > > > > > > b.co
> > > > > > > m_
> > > > > > > &d
> > > > > > > =D
> > > > > > > wIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67
> > > > > > > GvlG
> > > > > > > Zs
> > > > > > > tT
> > > > > > > py
> > > > > > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqj
> > > > > > > R05A
> > > > > > > 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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto
> > > > > > > :d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > > Sean.Finan@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=qS4goWBT7poplM
> > > > > > > > 69zy
> > > > > > > > _3
> > > > > > > > xh
> > > > > > > > Kw
> > > > > > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd
> > > > > > > > 4f7d
> > > > > > > > 4g
> > > > > > > > Ta
> > > > > > > > o&
> > > > > > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7X
> > > > > > > > XCD3
> > > > > > > > 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_3xhKwEW14JZMSdioCoppx
> > > > > > > > eFU&
> > > > > > > > r=
> > > > > > > > fs
> > > > > > > > 67
> > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_T
> > > > > > > > aKVF
> > > > > > > > qO
> > > > > > > > nS
> > > > > > > > Of
> > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24
> > > > > > > > gMo6 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_3xhKwEW14JZMSdioCoppx
> > > > > > > > eFU&
> > > > > > > > r=
> > > > > > > > fs
> > > > > > > > 67
> > > > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_T
> > > > > > > > aKVF
> > > > > > > > qO
> > > > > > > > nS
> > > > > > > > Of
> > > > > > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24
> > > > > > > > gMo6
> > > > > > > > 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.Miller@childrens.harvard.edu<mailto:T
> > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harva
> > > rd.e
> > > du
> > > >>]
> > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > to:d
> > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> bhagwat
> > .
> > > posane@gmail.com>>>
> > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mail
> > > > > > > > to:d
> > > ev@ctakes.apache.org<ma...@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=qS4goWBT7po
> > > > > > > > plM6
> > > > > > > > 9z
> > > > > > > > y_
> > > > > > > > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> > > > > > > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_
> > > > > > > > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCEN
> > > > > > > > aERN 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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > Gandhi.Natarajan@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_3xhKwEW14JZMSdioCop
> > > > > > > > > pxeF
> > > > > > > > > U&
> > > > > > > > > r=
> > > > > > > > > He
> > > > > > > > > up
> > > > > > > > > -I
> > > > > > > > > bs
> > > > > > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx667
> > > > > > > > > 4h&m
> > > > > > > > > =E
> > > > > > > > > fs
> > > > > > > > > fu
> > > > > > > > > j3
> > > > > > > > > 7p
> > > > > > > > > WN
> > > > > > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iya
> > > > > > > > > qEJz
> > > > > > > > > 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.posane@gmail.com
> > <mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:b
> > > hagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > ><ma...@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
>
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Hi Sean,
Unfortunately I haven't received it in spam folder too.
On Nov 15, 2017 7:47 PM, "Finan, Sean" <Se...@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.posane@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.posane@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.Miller@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 <bh...@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<ma...@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com>]
> > > Sent: Monday, November 13, 2017 3:25 AM
> > > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > > Sean.Finan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > Sent: Friday, November 10, 2017 6:13 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > > <ma...@childrens.harvard.edu><mailto:
> > > Sean.Finan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > > Sent: Thursday, November 09, 2017 9:06 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > > Sean.Finan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal
> > > > > .com
> > > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > > Sean.Finan@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.Miller@childrens.harvard.edu<mailto:T
> > > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.e
> > > du
> > > >>]
> > > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:
> bhagwat
> > .
> > > posane@gmail.com>>>
> > > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > > To:
> > > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > > Gandhi.Natarajan@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.posane@gmail.com
> > <mailto:
> > > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > > a
> > > t.posane@gmail.com>>]
> > > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > > ><ma...@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
>
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@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 <Se...@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.posane@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.Miller@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 <bh...@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<ma...@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com>]
> > Sent: Monday, November 13, 2017 3:25 AM
> > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > Sent: Friday, November 10, 2017 6:13 AM
> > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > <ma...@childrens.harvard.edu><mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > Sent: Thursday, November 09, 2017 9:06 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal
> > > > .com
> > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > Sean.Finan@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.Miller@childrens.harvard.edu<mailto:T
> > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.e
> > du
> > >>]
> > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwat
> .
> > posane@gmail.com>>>
> > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > Gandhi.Natarajan@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.posane@gmail.com
> <mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > ><ma...@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
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@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.posane@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.Miller@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 <bh...@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<ma...@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com>]
> > Sent: Monday, November 13, 2017 3:25 AM
> > To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > Sent: Friday, November 10, 2017 6:13 AM
> > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> > <ma...@childrens.harvard.edu><mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > Sent: Thursday, November 09, 2017 9:06 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > Sean.Finan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal
> > > > .com
> > ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > Gandhi.Natarajan@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> > childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> > Sean.Finan@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.Miller@childrens.harvard.edu<mailto:T
> > imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> > Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.e
> > du
> > >>]
> > > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwat
> .
> > posane@gmail.com>>>
> > > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > > To:
> > > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> > ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> > arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> > Gandhi.Natarajan@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.posane@gmail.com
> <mailto:
> > bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> > a
> > t.posane@gmail.com>>]
> > > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> > ><ma...@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@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 <Se...@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.Miller@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 <bh...@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<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> Sent: Monday, November 13, 2017 3:25 AM
> To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> Sean.Finan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> Sent: Friday, November 10, 2017 6:13 AM
> To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> <ma...@childrens.harvard.edu><mailto:
> Sean.Finan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> > Sent: Thursday, November 09, 2017 9:06 AM
> > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> Sean.Finan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal
> > > .com
> ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > To:
> > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> Sean.Finan@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.Miller@childrens.harvard.edu<mailto:T
> imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.e
> du
> >>]
> > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwat.
> posane@gmail.com>>>
> > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > To:
> > > > > > dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagw
> a
> t.posane@gmail.com>>]
> > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><ma...@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
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@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.Miller@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 <bh...@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<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> Sent: Monday, November 13, 2017 3:25 AM
> To: dev@ctakes.apache.org<ma...@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<ma...@childrens.harvard.edu><mailto:
> Sean.Finan@childrens.harvard.edu<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> Sent: Friday, November 10, 2017 6:13 AM
> To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> <ma...@childrens.harvard.edu><mailto:
> Sean.Finan@childrens.harvard.edu<mailto:Sean.Finan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> > Sent: Thursday, November 09, 2017 9:06 AM
> > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> Sean.Finan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@arisglobal.com
> ><mailto:Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> childrens.harvard.edu><mailto:Sean.Finan@childrens.harvard.edu<mailto:
> Sean.Finan@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.Miller@childrens.harvard.edu<mailto:T
> imothy.Miller@childrens.harvard.edu><mailto:Timothy.
> Miller@childrens.harvard.edu<mailto:Timothy.Miller@childrens.harvard.edu
> >>]
> > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwat.
> posane@gmail.com>>>
> > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > To: dev@ctakes.apache.org<ma...@ctakes.apache.org><mailto:d
> ev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> arisglobal.com><mailto:Gandhi.Natarajan@arisglobal.com<mailto:
> Gandhi.Natarajan@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com><mailto:bhagwat.posane@gmail.com<mailto:bhagwa
> t.posane@gmail.com>>]
> > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org
> ><ma...@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.Miller@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 <bh...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>]
Sent: Monday, November 13, 2017 3:25 AM
To: dev@ctakes.apache.org<ma...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>>]
Sent: Friday, November 10, 2017 6:13 AM
To: dev@ctakes.apache.org<ma...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>>]
> Sent: Thursday, November 09, 2017 9:06 AM
> To: dev@ctakes.apache.org<ma...@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
> <Se...@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.posane@gmail.com<ma...@gmail.com>>]
> > Sent: Wednesday, November 08, 2017 2:41 AM
> > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > To: dev@ctakes.apache.org<ma...@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
> > > > <Se...@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.Miller@childrens.harvard.edu<ma...@childrens.harvard.edu>>]
> > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > To: dev@ctakes.apache.org<ma...@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 <bh...@gmail.com>>>
> > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > To: dev@ctakes.apache.org<ma...@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
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
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:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/timeannotator/model.jar?view=log
and then update this java file:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java?view=markup
and recompile, and it should remove the error.
Tim
________________________________
From: Bhagwat Posane <bh...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>]
Sent: Monday, November 13, 2017 3:25 AM
To: dev@ctakes.apache.org<ma...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>>]
Sent: Friday, November 10, 2017 6:13 AM
To: dev@ctakes.apache.org<ma...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>>]
> Sent: Thursday, November 09, 2017 9:06 AM
> To: dev@ctakes.apache.org<ma...@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
> <Se...@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.posane@gmail.com<ma...@gmail.com>>]
> > Sent: Wednesday, November 08, 2017 2:41 AM
> > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > To: dev@ctakes.apache.org<ma...@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
> > > > <Se...@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.Miller@childrens.harvard.edu<ma...@childrens.harvard.edu>>]
> > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > To: dev@ctakes.apache.org<ma...@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 <bh...@gmail.com>>>
> > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>>]
> > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > To: dev@ctakes.apache.org<ma...@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@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.posane@gmail.com]
> Sent: Monday, November 13, 2017 3:25 AM
> To: 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<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> Sent: Friday, November 10, 2017 6:13 AM
> To: dev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu
> <ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> > Sent: Thursday, November 09, 2017 9:06 AM
> > To: dev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> 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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> > > Sent: Wednesday, November 08, 2017 2:41 AM
> > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> > > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> 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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> > > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > > To: dev@ctakes.apache.org<ma...@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.Finan@childrens.harvard.edu<mailto:Sean.Finan@
> 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.Miller@childrens.harvard.edu<mailto:T
> imothy.Miller@childrens.harvard.edu>]
> > > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > > To: dev@ctakes.apache.org<ma...@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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>>
> > > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<mailto:Gandhi.Natarajan@
> 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.posane@gmail.com<mailto:
> bhagwat.posane@gmail.com>]
> > > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > > To: dev@ctakes.apache.org<ma...@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@gmail.com]
Sent: Monday, November 13, 2017 3:25 AM
To: 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 <Se...@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.posane@gmail.com<ma...@gmail.com>]
Sent: Friday, November 10, 2017 6:13 AM
To: dev@ctakes.apache.org<ma...@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 <Se...@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.posane@gmail.com<ma...@gmail.com>]
> Sent: Thursday, November 09, 2017 9:06 AM
> To: dev@ctakes.apache.org<ma...@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
> <Se...@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.posane@gmail.com<ma...@gmail.com>]
> > Sent: Wednesday, November 08, 2017 2:41 AM
> > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>]
> > > Sent: Tuesday, November 07, 2017 3:22 PM
> > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>]
> > > > Sent: Friday, November 03, 2017 7:39 PM
> > > > To: dev@ctakes.apache.org<ma...@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
> > > > <Se...@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.Miller@childrens.harvard.edu<ma...@childrens.harvard.edu>]
> > > > > Sent: Monday, October 30, 2017 9:48 AM
> > > > > To: dev@ctakes.apache.org<ma...@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 <bh...@gmail.com>>
> > > > > Sent: Monday, October 30, 2017 7:24 AM
> > > > > To: dev@ctakes.apache.org<ma...@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.Natarajan@arisglobal.com<ma...@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.posane@gmail.com<ma...@gmail.com>]
> > > > > > Sent: Monday, October 30, 2017 4:30 PM
> > > > > > To: dev@ctakes.apache.org<ma...@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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,
[image: 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 <Se...@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.posane@gmail.com]
> Sent: Friday, November 10, 2017 6:13 AM
> To: 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.Finan@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.posane@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.Finan@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.posane@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.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.posane@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.Natarajan@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.posane@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.Finan@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.Miller@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 <bh...@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=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.Natarajan@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.posane@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
>
--
Thanks,
Bhagwat Posane
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@gmail.com]
Sent: Friday, November 10, 2017 6:13 AM
To: 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 <Se...@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.posane@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.Finan@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.posane@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.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.posane@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.Natarajan@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.posane@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.Finan@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.Miller@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 <bh...@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=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.Natarajan@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.posane@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@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.posane@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.Finan@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.posane@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.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.posane@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.Natarajan@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.posane@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.Finan@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.Miller@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 <bh...@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.Natarajan@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.posane@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@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 <Se...@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.posane@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.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.posane@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.Natarajan@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.posane@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.Finan@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.Miller@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 <bh...@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.Natarajan@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.posane@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@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.posane@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.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.posane@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.Natarajan@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_heal
> > > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=qS4go
> > > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r
> > > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=Wyt
> > > 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=fs67GvlGZstTpy
> > > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwq
> > > 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.posane@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.Finan@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_3xhKw
> > > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
> > > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3trfx4P
> > > > 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=fs67
> > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > > 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=fs67
> > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > > 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.Miller@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 <bh...@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.Natarajan@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=Efsfu
> > > > > j3
> > > > > 7p
> > > > > WN
> > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgCh
> > > > > 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.posane@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Argh,
The apache listserv occasionally ignores my line breaks:
// Times. There aren't default models, so set specifically add BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
Should be two lines (comment, then command):
// Times. There aren't default models, so set specifically
add BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
The same goes for the "load XXXXX YY=ZZ" statements that look like they are the ends of comment lines.
Sean
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 8:09 AM
To: dev@ctakes.apache.org
Subject: RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
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.posane@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.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.posane@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.Natarajan@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_heal
> > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=qS4go
> > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r
> > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=Wyt
> > 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=fs67GvlGZstTpy
> > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwq
> > 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.posane@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.Finan@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_3xhKw
> > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
> > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3trfx4P
> > > 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=fs67
> > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > 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=fs67
> > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > 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.Miller@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 <bh...@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.Natarajan@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=Efsfu
> > > > j3
> > > > 7p
> > > > WN
> > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgCh
> > > > 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.posane@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.posane@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.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.posane@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.Natarajan@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_heal
> > thnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=qS4go
> > WBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r
> > 0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=Wyt
> > 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=fs67GvlGZstTpy
> > IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwq
> > 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.posane@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.Finan@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_3xhKw
> > > EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
> > > m=Q-UMs2CriAdL_TaKVFqOnSOfqjR05AQWCnwqn6bOrBk&s=VdNz5x7XXCD3trfx4P
> > > 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=fs67
> > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > 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=fs67
> > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Q-UMs2CriAdL_TaKVFqOnSOf
> > > qjR05AQWCnwqn6bOrBk&s=1hU1X63Qu3ZRVgWTSJd9uxe-X5W-hKlf24gMo6GhJws&
> > > 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.Miller@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 <bh...@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.Natarajan@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=Efsfu
> > > > j3
> > > > 7p
> > > > WN
> > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgCh
> > > > 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.posane@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
Tim,
Thanks for the inputs. Your guess is absolutely correct.
Could you please tell me more about multiple components those are required
and how to use them to achieve the expected results.
On 8 November 2017 at 19:46, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> "if any procedure is happened or not."
>
> I think you need a formal definition of this to understand what you're
> trying to do.
>
> As a guess, you want it to be in the past, related to the patient (not a
> family member), and not negated or hypothetical or uncertain, etc.?
> This would require multiple components, but most of them should run in the
> temporal pipeline.
>
> Tim
> ________________________________________
> From: Bhagwat Posane <bh...@gmail.com>
> Sent: Wednesday, November 8, 2017 2:40 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.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.posane@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.Natarajan@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_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=
> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyaw
> dkxXvYuBFoonI&s=uGmJ4i-iqGkA8mjvWJoNlSm7QKjHyRhOtcsjI_Hvs70&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=DwIBaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyaw
> dkxXvYuBFoonI&s=N1LP2gEWWo6tF84sfvjw_hqRuW1fEdvqkBw7bM3VYzU&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.posane@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.Finan@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_
> 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyaw
> dkxXvYuBFoonI&s=sJCh70kfpVGg_2l3D7h6QYndeat50yHva5sNnmhVZbw&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=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyaw
> dkxXvYuBFoonI&s=oN0sRQQgrlsp8j926ayeysmYTVO2kriknuUjfIjlUq8&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=Heup-IbsIg9Q1TPOylpP9FE4GTK-
> OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyaw
> dkxXvYuBFoonI&s=oN0sRQQgrlsp8j926ayeysmYTVO2kriknuUjfIjlUq8&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.Miller@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 <bh...@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.Natarajan@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=Heup
> > > > > -I
> > > > > bs
> > > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj3
> > > > > 7p
> > > > > WN
> > > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsB
> > > > > 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.posane@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
Re: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
"if any procedure is happened or not."
I think you need a formal definition of this to understand what you're trying to do.
As a guess, you want it to be in the past, related to the patient (not a family member), and not negated or hypothetical or uncertain, etc.?
This would require multiple components, but most of them should run in the temporal pipeline.
Tim
________________________________________
From: Bhagwat Posane <bh...@gmail.com>
Sent: Wednesday, November 8, 2017 2:40 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.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.posane@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.Natarajan@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_healthnlp_examples_tree_master_ctakes-2Dtemporal-2Ddemo&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI&s=uGmJ4i-iqGkA8mjvWJoNlSm7QKjHyRhOtcsjI_Hvs70&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=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI&s=N1LP2gEWWo6tF84sfvjw_hqRuW1fEdvqkBw7bM3VYzU&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.posane@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.Finan@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_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI&s=sJCh70kfpVGg_2l3D7h6QYndeat50yHva5sNnmhVZbw&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=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI&s=oN0sRQQgrlsp8j926ayeysmYTVO2kriknuUjfIjlUq8&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=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI&s=oN0sRQQgrlsp8j926ayeysmYTVO2kriknuUjfIjlUq8&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.Miller@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 <bh...@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.Natarajan@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=Heup
> > > > -I
> > > > bs
> > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj3
> > > > 7p
> > > > WN
> > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsB
> > > > 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.posane@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
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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.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.posane@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.Natarajan@arisglobal.com> wrote:
>
> > Hi Bhagwat,
> >
> > I'm not sure if it will help you. But I extended the code available in
> > https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
> > to get the XML output and parsed the required mentions for me like
> > Procedure, Disorder etc.
> >
> > You can look at the code here - https://github.com/
> > 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.posane@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.Finan@childrens.harvard.edu
> > >
> > wrote:
> >
> > > Hi Bhagwat,
> > >
> > > If you are interested in the default clinical pipeline, you can look
> > > at the wiki here:
> > > https://cwiki.apache.org/confluence/display/CTAKES/
> > > 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://cwiki.apache.org/
> > > 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://cwiki.apache.org/
> > > 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.Miller@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 <bh...@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.Natarajan@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=Heup
> > > > -I
> > > > bs
> > > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj3
> > > > 7p
> > > > WN
> > > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsB
> > > > 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.posane@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
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.posane@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.Natarajan@arisglobal.com> wrote:
> Hi Bhagwat,
>
> I'm not sure if it will help you. But I extended the code available in
> https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
> to get the XML output and parsed the required mentions for me like
> Procedure, Disorder etc.
>
> You can look at the code here - https://github.com/
> 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.posane@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.Finan@childrens.harvard.edu
> >
> wrote:
>
> > Hi Bhagwat,
> >
> > If you are interested in the default clinical pipeline, you can look
> > at the wiki here:
> > https://cwiki.apache.org/confluence/display/CTAKES/
> > 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://cwiki.apache.org/
> > 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://cwiki.apache.org/
> > 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.Miller@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 <bh...@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.Natarajan@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=Heup
> > > -I
> > > bs
> > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj3
> > > 7p
> > > WN
> > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsB
> > > 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.posane@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.
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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.Natarajan@arisglobal.com> wrote:
> Hi Bhagwat,
>
> I'm not sure if it will help you. But I extended the code available in
> https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo to
> get the XML output and parsed the required mentions for me like Procedure,
> Disorder etc.
>
> You can look at the code here - https://github.com/
> 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.posane@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.Finan@childrens.harvard.edu
> >
> wrote:
>
> > Hi Bhagwat,
> >
> > If you are interested in the default clinical pipeline, you can look
> > at the wiki here: https://cwiki.apache.org/confluence/display/CTAKES/
> > 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://cwiki.apache.org/
> > 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://cwiki.apache.org/
> > 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.Miller@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 <bh...@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.Natarajan@arisglobal.com> wrote:
> >
> > > Hi Bhagwat,
> > >
> > > The source code of cTAKES is available under
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_
> > > re
> > > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-I
> > > bs
> > > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37p
> > > WN
> > > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsBLY
> > > 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.posane@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
RE: source code of user installation of cTakes. [EXTERNAL]
[SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Bhagwat,
I'm not sure if it will help you. But I extended the code available in https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo to get the XML output and parsed the required mentions for me like Procedure, Disorder etc.
You can look at the code here - https://github.com/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.posane@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 <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> If you are interested in the default clinical pipeline, you can look
> at the wiki here: https://cwiki.apache.org/confluence/display/CTAKES/
> 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://cwiki.apache.org/
> 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://cwiki.apache.org/
> 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.Miller@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 <bh...@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.Natarajan@arisglobal.com> wrote:
>
> > Hi Bhagwat,
> >
> > The source code of cTAKES is available under
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_
> > re
> > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-I
> > bs
> > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37p
> > WN
> > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsBLY
> > 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.posane@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.
Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]
Posted by Bhagwat Posane <bh...@gmail.com>.
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 <Se...@childrens.harvard.edu>
wrote:
> Hi Bhagwat,
>
> If you are interested in the default clinical pipeline, you can look at
> the wiki here: https://cwiki.apache.org/confluence/display/CTAKES/
> 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://cwiki.apache.org/
> 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://cwiki.apache.org/
> 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.Miller@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 <bh...@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.Natarajan@arisglobal.com> wrote:
>
> > Hi Bhagwat,
> >
> > The source code of cTAKES is available under
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> > pos_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-Ibs
> > Ig9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWN
> > oR_6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=O0hR4sqek-qxWLs6iyaqEJz4RPgChsBLYIC
> > 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.posane@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