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.pos...@gmail.com] Sent: Friday, November 03, 2017 7:39 PM To: dev@ctakes.apache.org Subject: Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS] Thank you Sean and Tim for your support. I have followed the links given by Sean and overview by Tim which is pretty helpful to get the better understanding of source code. I have run ctakes-example project that internally executes ClinicalPipelineFactory.getDefaultPipeline() method. This has given results like POS tag, Polarity, etc. Now, I am more interested in finding Procedure, Medication, Drug, etc. Could you please point me to the code file or help with code snippet to capture above terms. On 30 October 2017 at 19:36, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Bhagwat, > > If you are interested in the default clinical pipeline, you can look > at the wiki here: https://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.mil...@childrens.harvard.edu] > Sent: Monday, October 30, 2017 9:48 AM > To: dev@ctakes.apache.org > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > [SUSPICIOUS] > > cTAKES is based on Apache UIMA, which is a pipeline-building tool. So > the output you see in the CVD is the result of many different pieces > of the pipeline run in succession, and they are each in different > modules of cTAKES. ctakes-core has the most basic elements that will > run for every pipeline -- tokens, sentences, etc. > ctakes-dictionary-lookup-fast is what maps text spans to UMLS concepts. > ctakes-assertion finds negation status. > ctakes-chunker creates syntactic chunks and ctakes-pos-tagger finds > part-of-speech tags for tokens. There are many others but I think this > covers the basics. In general, if you see a type in the CVD that you > find interesting, your best bet is to grep the code for that type and > see where it is being created (if you don't want to wait for an email from > the list). > Pipeline components are known as "Analysis Engines" (AEs) in UIMA > lingo and as a result are often in a package ending in .ae. > Hope this helps you navigate the code! > Tim > > ________________________________________ > From: Bhagwat Posane <bhagwat.pos...@gmail.com> > Sent: Monday, October 30, 2017 7:24 AM > To: dev@ctakes.apache.org > Subject: Re: source code of user installation of cTakes. [EXTERNAL] > > Thanks Gandhi, for the quick response. > > I have source code of cTAKES which is available under > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn. > apache.org_repos_asf_ctakes_trunk&d=DwIBaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Efsfuj37pWNoR_ > 6AidMyWm4ab03VgFjoRDFcJxdS9k0&s=ZquL0hWuNhJGyujJCmNBTCENaERN6B > U3zisHhnM18Wo&e=. I see there are many projects in it. > > I am checking user version using \CTAKES_HOME\bin\runctakesCVD.bat, > this opens an UI. I could run analysis engine for a clinical note > according to the guidelines in the user-install guide.. > It gives me descent result in the left pane of the UI. > Now I am looking for the source-code that gives this result for a > clinical note. Could you please point me to the project, where can I > see to it in the ctakes-trunk or so. > > > > On 30 October 2017 at 16:36, Gandhi Rajan Natarajan < > gandhi.natara...@arisglobal.com> wrote: > > > Hi Bhagwat, > > > > The source code of cTAKES is available under > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.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.pos...@gmail.com] > > Sent: Monday, October 30, 2017 4:30 PM > > To: dev@ctakes.apache.org > > Subject: source code of user installation of cTakes. > > > > Hello, > > > > I have seen the results of user installation of cTakes , the output > > is pretty interesting. > > > > Can anybody point to the source code of the same? > > > > I have just started exploring this project if anybody point me to > > good resources to understand it thoroughly that will be great help....!! > > > > I have downloaded the developer installation too. > > > > -- > > Thanks, > > Bhagwat Posane > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they > > are > addressed. > > If you are not the named addressee you should not disseminate, > > distribute or copy this e-mail. Please notify the sender or system > > manager by email immediately if you have received this e-mail by > > mistake and delete this e-mail from your system. If you are not the > > intended recipient you are notified that disclosing, copying, > > distributing or taking any action in reliance on the contents of > > this information is strictly prohibited and against the law. > > > > > > -- > Thanks, > Bhagwat Posane > -- Thanks, Bhagwat Posane This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. 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