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Posted to dev@ctakes.apache.org by Bhagwat Posane <bh...@gmail.com> on 2017/12/04 17:02:40 UTC
Re: Interpret context out of clinical note [EXTERNAL]
Hello Sean, et al,
Does anyone have chance to update on my issues mentioned in thread ?
On 29 November 2017 at 18:35, Bhagwat Posane <bh...@gmail.com>
wrote:
> Sure, Sean. Please !
>
> On 28 November 2017 at 23:16, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
>
>> Hi Bhagwat,
>>
>> I will try to answer this over the next day or two. Somebody else may
>> have some free time and get to you first ...
>>
>> Sean
>>
>> -----Original Message-----
>> From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> Sent: Tuesday, November 28, 2017 12:11 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: Interpret context out of clinical note [EXTERNAL]
>>
>> Hello Sean,
>>
>> Thank you very much for your patience and bare with my basic queries.
>>
>> 1) What information you are trying to obtain from a note. An example
>> sentence would help.
>>
>> >> Here are some example sentence from which I want to make out weather
>> >> cystoscopy
>> is done or not.
>> >> ex:
>> Note 1:
>> In addition he has bilateral stones, non-obstructing and bilateral renal
>> cysts. I have been recommended that he
>> obtain a CT scan for staging, office cystoscopy for diagnosis, and
>> subsequently a bladder biopsy excision of the bladder tumor.
>> ----> cystoscopy not done
>>
>>
>> Note 2:
>> He has incidental bilateral renal stones 4.4 mm on the right and 2 mm on
>> the left. Cystoscopy showed a bladder
>> tumor on the floor of the bladder right side sessile 3 cm. suspicious for
>> invasion . Biopsy showed no invasion but high grade.
>> ---> cystoscopy done
>>
>>
>> Note 3:
>> Cystoscopy 2/10/16 shows the fistula, BPH, and no bladder lesions. Will
>> proceed with the fistula closure. CT
>> DONE IN THE HOSPITAL 2/24/16 SHOWED INVASIVE BLADDER CANCER INTRA-MURAL
>> OBSTRUCTING BOTH KIDNEYS. PATIENT WILL REQURIE A CYSTECTOMY AND URINARY
>> DIVERSION.
>> ---> Cystoscopy done / CYSTECTOMY not done
>>
>>
>> Note 4:
>> Other medical history in this patient includes diabetes, high blood
>> pressure. Surgical history includes gallbladder,
>> liver biopsy, bladder tumor resection as stated above. Return in 12
>> mos.
>> for repeat cystoscopy.
>> ---> cystoscopy done
>>
>>
>> Note 5:
>> Medical history in this patient is left blank except for thyroid disease.
>> Surgical history includes some hand
>> surgery. He also had some kind of eye surgery in 1987. Plan will be
>> cystoscopy, resection of bladder tumor for staging and retrograde
>> pyelogram. This is scheduled to be done at Medical City on July 20 at 7:30
>> in the morning.
>> ----> cystoscopy done
>>
>> ************************************************************
>> ************************************************************
>> ********************************************************************
>>
>> 2) What you have already done to successfully or unsuccessfully obtain
>> the information.
>>
>> >> I had checked outputs on web api of ctakes by giving some notes, I
>> suspected TLINK must be helpful component to get the above work done.
>> >> so I followed the path how to get the TLINK statement output and I
>> achieved it using piper file.
>>
>> ************************************************************
>> ************************************************************
>> ********************************************************************
>>
>> 3) What you do understand at this point in time.
>> >> I understood only how to run particular pipeline using piper file and
>> get the output in HTML file.
>> >> I have gone through the ctakes-wiki, I have brief idea about each
>> module.
>>
>> ************************************************************
>> ************************************************************
>> ********************************************************************
>>
>> 4) What you think is missing from your understanding.
>> >>Till now I had thought of using TLINKS to capture the context out of
>> note. I think so because of categories in TLINKS. After fetching TLINKS
>> in HTML format, while interpreting context, I feel mere TLINK wont help and
>> I need something else to get my work done.
>> >>At present I think I am lost somewhere and not able to figure out the
>> pipeline that needs to be used to get my work done
>>
>> ************************************************************
>> ************************************************************
>> ********************************************************************
>> 5) What you really need from us. A workflow? A pipeline? Pointers
>> toward existing code? Pointers toward datatypes? A deeper explanation of
>> existing code (pick 1 class)? Help writing new ctakes code of your own?
>>
>> >> More precisely, I need a pipeline to do above task, and deeper
>> explanation of code of this pipeline. Having code insight I will have a
>> better control on the output, i.e. instead of having output in xmi/html, I
>> can prepare collection or so for the output. This may need to write new
>> cTakes code, not sure though.
>>
>>
>>
>> On 27 November 2017 at 19:02, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu>
>> wrote:
>>
>> > Hi Bhagwat.
>> >
>> > You wrote:
>> > > Now coming back to our original question for which this thread has
>> > > been
>> > initiated.
>> > > I was trying to get the context out of clinical notes. for ex. If
>> > > any
>> > procedure is happened or not on patient.
>> > > ...
>> > > By following this clues, I am nowhere.
>> > > Could you please provide information on which pipeline I should have
>> > > to
>> > run to achieve this goal, and how?
>> >
>> > Your snippet of my previous message is incomplete. The sentence that
>> > I wrote following what you copied was:
>> > --- In those files each "add" statement is followed by an annotator
>> > class name.
>> >
>> > Those were your clues. Those annotator classes provide the information
>> > that you were asking about. Here are the contents of the
>> > AttributeClearTkSubPipe.piper:
>> > ==========================================
>> > // Commands and parameters to create a default entity attributes
>> > processing sub-pipeline. This is not a full pipeline.
>> >
>> > // Add the Dependency parser for use by cleartk addDescription
>> > ClearNLPDependencyParserAE // Add the Semantic Role Labeler parser for
>> > use by cleartk addLogged ClearNLPSemanticRoleLabelerAE
>> >
>> > // Add the cleartk package for cleartk class lookups package
>> > org.apache.ctakes.assertion.medfacts.cleartk
>> >
>> > // Add the cleartk attribute engines, logging for them as a block add
>> > StartFinishLogger LOGGER_NAME=CleartkAnalysisEngine
>> > LOGGER_TASK="Assigning Attributes" IS_START=true addDescription
>> > PolarityCleartkAnalysisEngine addDescription
>> > UncertaintyCleartkAnalysisEngine addDescription
>> > HistoryCleartkAnalysisEngine addDescription
>> > ConditionalCleartkAnalysisEngine addDescription
>> > GenericCleartkAnalysisEngine addDescription
>> > SubjectCleartkAnalysisEngine add StartFinishLogger
>> > LOGGER_NAME=CleartkAnalysisEngine LOGGER_TASK="Assigning Attributes"
>> > ==========================================
>> >
>> > The comments in the file provide hints, and the names of the annotator
>> > classes should give an even greater indication of function.
>> "PolarityCleartkAnalysisEngine"
>> > assigns polarity (negation), "UncertaintyCleartkAnalysisEngine"
>> > assigns uncertainty, etc.
>> >
>> > It is far from exhaustive, but you should always browse the ctakes
>> > wiki before posting to the dev list. The page on Assertion:
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
>> > confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BAssertion&d=DwIBaQ&c=qS
>> > 4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6
>> > r0bcpKGd4f7d4gTao&m=xI09LL4AitA-w9uu3DF3OBqlDGFKNeuB7wCAi5UxnYY&s=7oBh
>> > A5oVMUlUqetkOGeynSeay1WE4SnfhRU9agGr8gs&e=
>> >
>> > If you visit the page on the default clinical pipeline you will see
>> > that it extracts negation, uncertainty and subject (right at the top,
>> > plus a diagram).
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
>> > confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
>> > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xI09LL4Ait
>> > A-w9uu3DF3OBqlDGFKNeuB7wCAi5UxnYY&s=HOuzDHk2YB6nz0Lm-E0TR2oSxUA-j30dPj
>> > 4PXUR-aeY&e=
>> > Default+Clinical+Pipeline
>> >
>> > Near the bottom of that wiki page is stated "... runClinicalPipeline
>> > runs the piper file DefaultFastPipeline.piper ...", and "piper file" is
>> a link.
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
>> > confluence_display_CTAKES_Piper-2BFiles&d=DwIBaQ&c=qS4goWBT7poplM69zy_
>> > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
>> > &m=xI09LL4AitA-w9uu3DF3OBqlDGFKNeuB7wCAi5UxnYY&s=c2wUBjNt1mjoFtkAx1kKb
>> > nDiMv7PSkXF5HBv1j-pOXg&e=
>> >
>> > Near the bottom of the piper files wiki page is a diagram of the
>> > DefaultFastPipeline.piper that clearly indicates that it uses the
>> > AttributeClearTkSubPipe.piper, and it even lists the contents (as
>> > above) of that sub-pipeline.
>> >
>> > So, I am really confused as to what information you really want. You
>> > actually started this topic with:
>> > > 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?
>> >
>> > Gandi pointed you towards the ctakes source repository.
>> >
>> > You apparently got the source code for ctakes, and then stated:
>> > > Now I am looking for the source-code that gives this result for a
>> > clinical note.
>> >
>> > Tim pointed you to Apache UIMA and the different modules that make up
>> > the default clinical pipeline.
>> > I pointed you toward the wiki page for some additional information.
>> >
>> > You then stated:
>> > > 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 ...
>> >
>> > At this point Gandhi pointed to some helpful code.
>> >
>> > Then later you asked about temporal links because you thought that you
>> > needed them to provide certain information.
>> > > 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.
>> >
>> > Tim (correctly) stated that you might be more interested in
>> > event/entity attributes such as negation and pointed you towards
>> > modules that make up the default pipeline.
>> >
>> > Then, in your last message you ask:
>> > > Could you please provide information on which pipeline I should have
>> > > to
>> > run to achieve this goal, and how?
>> >
>> > Since we seem to have gone back and forth on this, I think that it
>> > might help everybody trying to help you if you could start over and
>> clearly state:
>> > 1) What information you are trying to obtain from a note. An example
>> > sentence would help.
>> > 2) What you have already done to successfully or unsuccessfully obtain
>> > the information.
>> > 3) What you do understand at this point in time.
>> > 4) What you think is missing from your understanding.
>> > 5) What you really need from us. A workflow? A pipeline? Pointers
>> > toward existing code? Pointers toward datatypes? A deeper
>> > explanation of existing code (pick 1 class)? Help writing new ctakes
>> code of your own?
>> >
>> >
>> > Thank you,
>> > Sean
>> >
>> >
>> > -----Original Message-----
>> > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> > Sent: Monday, November 27, 2017 12:49 AM
>> > To: dev@ctakes.apache.org
>> > Subject: Re: Interpret context out of clinical note [EXTERNAL]
>> >
>> > Hello Sean,
>> >
>> > Thank you for the inputs, Now coming back to our original question for
>> > which this thread has been initiated.
>> >
>> > I was trying to get the context out of clinical notes. for ex. If any
>> > procedure is happened or not on patient.
>> >
>> > To achieve this you mentioned some points :
>> >
>> > You can visit the ctakes-assertion-res module for some clues.
>> > > Navigate to ctakes-assertion-res src/main/resources/
>> > > org/apache/ctakes/assertion/pipeline/
>> > > There are two .piper files there. Each one covers a different way
>> > > to get the information that you mentioned.
>> >
>> >
>> > By following this clues, I am nowhere.
>> > Could you please provide information on which pipeline I should have
>> > to run to achieve this goal, and how?
>> >
>> >
>> > On 24 November 2017 at 21:24, Finan, Sean <Sean.Finan@childrens.harvard.
>> > edu>
>> > wrote:
>> >
>> > > Hi Bhagwat,
>> > >
>> > > Ok, a couple of things are problematic.
>> > >
>> > > 1. the DefaultFastPipeline already contains attribute detection
>> > > using the AttributeClearTkSubPipe.piper. That sub- pipeline adds
>> > > the ClearNLPSemanticRoleLabelerAE. So does the
>> AssertionSubPipe.piper.
>> > > The pipeline cannot have two instances of that annotator. The fix
>> > > for this is to just add the AssertionEngines that are at the bottom
>> > > of the AssertionSubPipe.piper.
>> > >
>> > > 2. The assertion engines don't work. They will spit out some log
>> > > messages about not being usable until ctakes-76 is implemented.
>> > > Then you will get a NullPointerException and ctakes will happily
>> crash.
>> > >
>> > > James Masanz made the last comment on ctakes-76:
>> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
>> > > rg
>> > > _jira_browse_CTAKES-2D76&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
>> > > di
>> > > oCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=wGmqUbPS3-
>> > > WJ
>> > > RSYmkNbjZ1e-OfMJTOVk6wbzOElQUrE&s=ZyPD1MbOImp08cCdSo0HeecCXAqUatZEZm
>> > > hA
>> > > W-cJVtc&e=
>> > > which includes the information:
>> > > "when this issue gets resolved (the jars are available from maven
>> > > central) then ctakes-assertion could be updated again to use"
>> > >
>> > > So, what to do?
>> > > Well, my advice would be to just skip the Assertion engines. The
>> > > default ClearTk attribute engines will produce the same types of
>> > > event and entity attributes and they are already in the default
>> pipeline.
>> > > Is there a reason that you wanted to use the older Assertion engines?
>> > > Was it just listed in (unfortunately) outdated documentation?
>> > >
>> > > Sean
>> > >
>> > >
>> > > -----Original Message-----
>> > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> > > Sent: Friday, November 24, 2017 8:58 AM
>> > > To: dev@ctakes.apache.org
>> > > Subject: Re: Interpret context out of clinical note [EXTERNAL]
>> > >
>> > > Hello Sean,
>> > >
>> > > As you mentioned in previous email The annotators in the Assertion
>> > > piper require several other annotators to run first, so to run
>> > > AssertionSubPipe.piper I have added DefaultFastPipeline and
>> > > AssertionDefaults piper file before that.
>> > >
>> > > for reference below text is from my piper file:
>> > >
>> > > ************************************************************
>> > > *********************
>> > > reader FileTreeReader InputDirectory=D:\Bhagwat\Notes load
>> > > org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
>> > > load org/apache/ctakes/examples/pipeline/AssertionDefaults.piper
>> > > load AssertionSubPipe.piper
>> > >
>> > > // Temporal (event, time, dtr, tlink) load TemporalSubPipe.piper
>> > >
>> > > // Html output
>> > > set OutputDirectory=D:\Bhagwat\HTMLoutput
>> > > add pretty.html.HtmlTextWriter
>> > >
>> > > //XMI output
>> > > //writeXmis D:\Bhagwat\XMI
>> > > ************************************************************
>> > > *********************
>> > >
>> > > As I run this piper file the command addLogged
>> > > ClearNLPSemanticRoleLabelerAE It is showing started processing....
>> > > and never finished. when I debugged the code I found it is going in
>> > > infinite loop for one of the sentence from clinical note.
>> > >
>> > > The code which goes in Infinite loop is in DEPNode.class file
>> > > ************************************************************
>> > > ************************************************************
>> > > ********************
>> > > public boolean isDescendentOf(DEPNode node) { DEPNode head =
>> > > getHead(); while (head != null) { if (head == node) return true;
>> > > head = head.getHead(); } return false; }
>> > > ************************************************************
>> > > ************************************************************
>> > > ********************
>> > > if (head == node) this condition never becomes true !
>> > >
>> > >
>> > > I have added clinical notes for your reference,for the highlighted
>> > > line the ClearNLPSemanticRoleLablerAE goes in infinite loop.
>> > >
>> > > ************************************************************
>> > > ************************************************************
>> > > *********************
>> > > Note 1:
>> > > The patient is XX years old with gross hematuria beginning ten days
>> ago.
>> > > He has pain over the bladder.
>> > > He smoked until XXXX. His country of origin is XXXX. He has been
>> > > here for two years.
>> > > Ultrasound is planned on 3/26/2015 shows a mass in the bladder 3.4
>> > > x
>> > > 3.8 x
>> > > 3.1 cm.
>> > >
>> > >
>> > >
>> > > Note 2:
>> > > This is a 67-year-old patient followed for erectile dysfunction and
>> > benign
>> > > prostatic hyperplasia. Prostate symptoms consist of slow stream
>> and
>> > NX
>> > > X 2. TUMT explained to the patient.
>> > > Urinalysis showed 2+ sugar before and trace of blood. No retention,
>> > > burning or blood. He is up perhaps once at night to void depending
>> > > upon his fluid
>> > > intake. PSA was .3 on 1/12.
>> > > The patient use to take AndroGel squirt three a day. T was 483 in Nov.
>> > > 2011. T was 531 on 1/13 by internist. He has been off the Androgel.
>> > > Testosterone is rechecked. He may choose to use IM testosterone at
>> home
>> > > self administered. He also uses TriMix for ED.
>> > > He has diminished number and frequency of erections. Duration is
>> years.
>> > > Modifying factors include Diabetes. Severity is 8 of 10. He no
>> > > logner uses Dialis. TriMix refilled.
>> > > Patient has lost 40 lbs on Victosa administered by his
>> endocrinologist.
>> > >
>> > > ************************************************************
>> > > ************************************************************
>> > > *********************
>> > >
>> > > The Interesting thing is when I run only the highlighted sentence as
>> > > a note it executes successfully, it means to get into infinite loop
>> > > the highlighted sentence should have at least one sentence with it.
>> > > Could you please provide your thoughts on it.
>> > >
>> > > Sorry for lengthy explanation, but I thought it is necessary.
>> > >
>> > >
>> > >
>> > > On 24 November 2017 at 01:22, Finan, Sean
>> <Sean.Finan@childrens.harvard.
>> > > edu>
>> > > wrote:
>> > >
>> > > > Hi Bhagwat,
>> > > >
>> > > > Thanks for the heads up on the "file:" issue. I will check to see
>> > > > if the usage has changed and fix the piper.
>> > > >
>> > > > Sean
>> > > >
>> > > > -----Original Message-----
>> > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> > > > Sent: Thursday, November 23, 2017 9:17 AM
>> > > > To: dev@ctakes.apache.org
>> > > > Subject: Re: Interpret context out of clinical note [EXTERNAL]
>> > > >
>> > > > Thanks James, It worked using cast to Map. !
>> > > >
>> > > > Sean,
>> > > > In AssertionDefaults.piper you set the file like:
>> > > >
>> > > > set
>> > > > assertionModelResource=file:org/apache/ctakes/assertion/mode
>> ls/i2b2.
>> > > > mo
>> > > > del
>> > > >
>> > > > As I run this piper file it throws file not found exception, it
>> > > > resolved for me by removing "file:" from command, I suppose this
>> > > > needs
>> > > to be fixed.
>> > > >
>> > > >
>> > > > On 22 November 2017 at 23:21, Finan, Sean
>> > <Sean.Finan@childrens.harvard.
>> > > > edu>
>> > > > wrote:
>> > > >
>> > > > > Wow, that is really strange.
>> > > > >
>> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache
>> > > > > .o
>> > > > > rg
>> > > > > _d
>> > > > > _uimafit-2Dcurrent_api_org_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwE
>> > > > > W1
>> > > > > 4J
>> > > > > ZM
>> > > > > SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1A9
>> > > > > as
>> > > > > f1
>> > > > > ga
>> > > > > bEGz-5fQfVfXbp2BcZEJaZIiJ4zSk09P1M&s=jo0yN7BJTt98IHerLXLK4aQvmSO
>> > > > > An
>> > > > > 90
>> > > > > pU
>> > > > > lzHg00ynFI&e=
>> > > > > apache/uima/fit/util/JCasUtil.html
>> > > > >
>> > > > >
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: James Masanz [mailto:masanz.james@gmail.com]
>> > > > > Sent: Wednesday, November 22, 2017 12:50 PM
>> > > > > To: dev@ctakes.apache.org
>> > > > > Subject: Re: Interpret context out of clinical note [EXTERNAL]
>> > > > >
>> > > > > If I use Eclipse, at build time I also get the error
>> > > > >
>> > > > > method putAll(Map<? extends Annotation,? extends
>> > > > > List<IdentifiedAnnotation>>) in the type Map<Annotation,List<
>> > > > > IdentifiedAnnotation>>
>> > > > > is not applicable for the arguments (Map)
>> > > > >
>> > > > > I haven't looked into why.
>> > > > >
>> > > > > A quick workaround is to add a cast to Map
>> > > > >
>> > > > > allCovering.putAll( (Map)JCasUtil.indexCovering( jCas, covered,
>> > > > > covering ) );
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > On Wed, Nov 22, 2017 at 8:40 AM, Finan, Sean <
>> > > > > Sean.Finan@childrens.harvard.edu> wrote:
>> > > > >
>> > > > > > Hi Bhagwat,
>> > > > > >
>> > > > > > I have no idea what is going on with your system.
>> > > > > >
>> > > > > > > The method putAll(Map<? extends Annotation,? extends
>> > > > > > > List<IdentifiedAnnotation>>) in the type
>> > > > > > > Map<Annotation,List<IdentifiedAnnotation>> is not applicable
>> > > > > > > for the arguments (Map)
>> > > > > >
>> > > > > > That doesn't make any sense to me. That is exactly what
>> > > > > > putAll is for ... Unless your uimafit does not return a typed
>> > > > > > map? In which case it is an old version? I am not sure how
>> > > > > > that would
>> > > happen.
>> > > > > >
>> > > > > > > When I run AssertionSubPipe.piper I am getting below error:
>> > > > > > The .piper files should all have line comments in them. The
>> > > > > > *SubPipe pipers should all have something like "This is not a
>> > > > > > complete pipeline" at the top. This means that it cannot be
>> > > > > > run alone. The annotators in the Assertion piper require
>> > > > > > several other annotators to run first. In addition to the
>> > > > > > default clinical piper I think that there are some piper files
>> > > > > > in ctakes-example-res that you can look at to
>> > > > > start.
>> > > > > >
>> > > > > > >, I don't find any variables value in understandable format
>> > > > > > >like (JCas
>> > > > > > jcas) object. How would I understand JCas object values?
>> > > > > >
>> > > > > > ctakes is built upon the Apache UIMA framework.
>> > > > > >
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apac
>> > > > > > he
>> > > > > > .o
>> > > > > > rg
>> > > > > > _&
>> > > > > > d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
>> > > > > > vl
>> > > > > > GZ
>> > > > > > st
>> > > > > > Tp
>> > > > > > yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=rVKcbkbznwk6V-PLUy56sA4hGgN0F
>> > > > > > 4q
>> > > > > > rL
>> > > > > > N5 Ik 6FIDnM&s=ebIFQbW0D4VLpTWv9a4YQqy_G30S_hDeDEbhCTesFuk&e=
>> > > > > >
>> > > > > > This should probably be on our wiki ... Anyway, the best way
>> > > > > > to learn about how ctakes pipelines are put together and how
>> > > > > > data is passed is to read some of the intro documentation for
>> uima.
>> > > > > >
>> > > > > > The Javadoc for jcas is here:
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apac
>> > > > > > he
>> > > > > > .o
>> > > > > > rg
>> > > > > > _d
>> > > > > > _&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs6
>> > > > > > 7G
>> > > > > > vl
>> > > > > > GZ
>> > > > > > st
>> > > > > > TpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=rVKcbkbznwk6V-PLUy56sA4hGgN
>> > > > > > 0F
>> > > > > > 4q
>> > > > > > rL
>> > > > > > N5 Ik6FIDnM&s=I_7BH2bDGR48vI03bE1dirKGCgq33PKB9vXN2VDrMA8&e=
>> > > > > > uimaj-current/apidocs/org/apache/uima/jcas/JCas.html
>> > > > > >
>> > > > > > Sean
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > -----Original Message-----
>> > > > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> > > > > > Sent: Wednesday, November 22, 2017 3:38 AM
>> > > > > > To: dev@ctakes.apache.org
>> > > > > > Subject: Re: Interpret context out of clinical note [EXTERNAL]
>> > > > > >
>> > > > > > Hello Sean,
>> > > > > >
>> > > > > > Thank you for the inputs. I have gone through both the piper
>> > > > > > files which you have mentioned.
>> > > > > >
>> > > > > > When I run AssertionSubPipe.piper I am getting below error:
>> > > > > >
>> > > > > > ////////////////////////////////////////////////////////////
>> > > > > > ////////////////////////////////////////////////////////////
>> > > > > > ////////////////////////////////////////////
>> > > > > >
>> > > > > > 22 Nov 2017 12:55:31 WARN SingleDocumentProcessor - This
>> > > > > > class cannot be used until CTAKES-76 is implemented.
>> > > > > > 22 Nov 2017 12:55:31 WARN SingleDocumentProcessor - This
>> > > > > > class cannot be used until CTAKES-76 is implemented.
>> > > > > > Nov 22, 2017 12:55:31 PM
>> > > > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_i
>> > > > > > mp
>> > > > > > l
>> > > > > > callAnalysisComponentProcess(430)
>> > > > > > SEVERE: Exception occurred
>> > > > > > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> > > > > > Annotator processing failed.
>> > > > > > at org.apache.uima.analysis_engine.impl.
>> > > PrimitiveAnalysisEngine_impl.
>> > > > > > callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java
>> > > > > > :4
>> > > > > > 12
>> > > > > > ) at
>> > > > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine
>> _impl.
>> > > > > > processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314
>> > > > > > ) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > > > > AggregateCasIterator.
>> > > > > > processUntilNextOutputCas(ASB_impl.java:570)
>> > > > > > at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > > > > > AggregateCasIterator.<init>(ASB_impl.java:412)
>> > > > > > at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
>> > > > > > process(ASB_impl.java:344)
>> > > > > > at org.apache.uima.analysis_engine.impl.
>> > > AggregateAnalysisEngine_impl.
>> > > > > > processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265
>> > > > > > ) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > > > > AggregateCasIterator.
>> > > > > > processUntilNextOutputCas(ASB_impl.java:570)
>> > > > > > at org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > > > > > AggregateCasIterator.<init>(ASB_impl.java:412)
>> > > > > > at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
>> > > > > > process(ASB_impl.java:344)
>> > > > > > at org.apache.uima.analysis_engine.impl.
>> > > AggregateAnalysisEngine_impl.
>> > > > > > processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265
>> > > > > > )
>> > > > > > at
>> > > > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.pr
>> > > > > > oc
>> > > > > > es
>> > > > > > s(
>> > > > > > AnalysisEngineImplBase.java:269) at
>> > > > > > org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(
>> > > > > > SimplePipeline.java:150)
>> > > > > > at org.apache.ctakes.core.pipeline.PipelineBuilder.run(
>> > > > > > PipelineBuilder.java:348)
>> > > > > > at org.apache.ctakes.core.pipeline.PiperFileRunner.run(
>> > > > > > PiperFileRunner.java:72)
>> > > > > > at org.apache.ctakes.core.pipeline.PiperFileRunner.main(
>> > > > > > PiperFileRunner.java:30)
>> > > > > > Caused by: java.lang.NullPointerException at
>> > > > org.apache.ctakes.assertion.
>> > > > > > medfacts.AssertionAnalysisEngineFit.process(
>> > > > > > AssertionAnalysisEngineFit.java:145)
>> > > > > > at
>> > > > > > org.apache.uima.analysis_component.JCasAnnotator_ImplBase.proc
>> > > > > > es
>> > > > > > s(
>> > > > > > JCasAnnotator_ImplBase.java:48) at
>> > > > > > org.apache.uima.analysis_engine.impl.
>> > > PrimitiveAnalysisEngine_impl.
>> > > > > > callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java
>> > > > > > :3
>> > > > > > 96
>> > > > > > )
>> > > > > > ... 14 more
>> > > > > >
>> > > > > > ////////////////////////////////////////////////////////////
>> > > > > > ////////////////////////////////////////////////////////////
>> > > > > > ////////////////////////////////////////////////////////////
>> > > > > > ///////////////////////
>> > > > > >
>> > > > > > The error is causing due to the command : add
>> > > > > > AssertionAnalysisEngineFit I have comment out this command and
>> > > > > > ran it, the html output doesn't have any difference with
>> > > > > > previous
>> > output.
>> > > > > > Could you please help me to resolve this error.
>> > > > > >
>> > > > > >
>> > > > > > On 21 November 2017 at 18:43, Finan, Sean
>> > > > <Sean.Finan@childrens.harvard.
>> > > > > > edu>
>> > > > > > wrote:
>> > > > > >
>> > > > > > > Hi Bhagwat,
>> > > > > > >
>> > > > > > > You can visit the ctakes-assertion-res module for some clues.
>> > > > > > >
>> > > > > > > Navigate to ctakes-assertion-res src/main/resources/
>> > > > > > > org/apache/ctakes/assertion/pipeline/
>> > > > > > >
>> > > > > > > There are two .piper files there. Each one covers a
>> > > > > > > different way to get the information that Tim mentioned. In
>> > > > > > > those files
>> > > each "add"
>> > > > > > > statement is followed by an annotator class name. In
>> > > > > > > IntelliJ you can press CTRL-N and enter the class name to
>> view the code.
>> > > > > > > There are also a few comments in the piper files that may
>> help.
>> > > > > > >
>> > > > > > > Sean
>> > > > > > >
>> > > > > > > -----Original Message-----
>> > > > > > > From: Bhagwat Posane [mailto:bhagwat.posane@gmail.com]
>> > > > > > > Sent: Tuesday, November 21, 2017 6:21 AM
>> > > > > > > To: dev@ctakes.apache.org
>> > > > > > > Subject: Interpret context out of clinical note [EXTERNAL]
>> > > > > > >
>> > > > > > > Hello Sean,Tim, et al,
>> > > > > > >
>> > > > > > > I would like to Interpret context out of clinical note, e.g.
>> > > > > > > interpretation of the procedure, lab tests for a patient.
>> > > > > > > For this, I suppose TLINK statements would be of much help.
>> > > > > > >
>> > > > > > > Ex. for the note- "Cystoscopy is planned on 3 / 26 / 2018."
>> > > > > > > I get TLINK as
>> > > > > > > Cystoscopy contains 3 / 26 / 2018,
>> > > > > > > 3 / 26 / 2018 contains Cystoscopy
>> > > > > > > 3 / 26 / 2018 contains planned we can make out that
>> > > > > > > Cystoscopy is not yet done looking at "planned"(in this
>> > > > > > > case),
>> > > > > > >
>> > > > > > > Could you please let me know if I am on right path and also
>> > > > > > > help me understand if any other approach to do this.
>> > > > > > >
>> > > > > > >
>> > > > > > > @Tim,
>> > > > > > > Couple of days back you mentioned about the context
>> > understanding :
>> > > > > > >
>> > > > > > > "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
>> > > > > > >
>> > > > > > >
>> > > > > > > Could you please provide some insight on this, as what are
>> > > > > > > the multiple components are required and how to use them to
>> > > > > > > achieve this
>> > > > > > goal.
>> > > > > > >
>> > > > > > > --
>> > > > > > > Thanks,
>> > > > > > > Bhagwat Posane
>> > > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > --
>> > > > > > Thanks,
>> > > > > > Bhagwat Posane
>> > > > > >
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Thanks,
>> > > > Bhagwat Posane
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Thanks,
>> > > Bhagwat Posane
>> > >
>> >
>> >
>> >
>> > --
>> > Thanks,
>> > Bhagwat Posane
>> >
>>
>>
>>
>> --
>> Thanks,
>> Bhagwat Posane
>>
>
>
>
> --
> Thanks,
> Bhagwat Posane
>
--
Thanks,
Bhagwat Posane