Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 1341D10929 for ; Tue, 11 Mar 2014 16:17:04 +0000 (UTC) Received: (qmail 91570 invoked by uid 500); 11 Mar 2014 16:17:03 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 91455 invoked by uid 500); 11 Mar 2014 16:17:02 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 91198 invoked by uid 99); 11 Mar 2014 16:17:01 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 11 Mar 2014 16:17:01 +0000 X-ASF-Spam-Status: No, hits=1.7 required=5.0 tests=FREEMAIL_ENVFROM_END_DIGIT,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of ravigarg27@gmail.com designates 209.85.215.52 as permitted sender) Received: from [209.85.215.52] (HELO mail-la0-f52.google.com) (209.85.215.52) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 11 Mar 2014 16:16:57 +0000 Received: by mail-la0-f52.google.com with SMTP id ec20so5742672lab.39 for ; Tue, 11 Mar 2014 09:16:35 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=2W15SVvSkI/vCUGEbjVzXxADwN+9eYODsFty5FLdbVM=; b=XbTDDgBgB8m6QpqQL+y7x9PofQK4nNyogCyixHeeObu3N78m9nqAnNhoFfFYxOnsL8 wwvk86NWUyTkAoA3uC0AyQCzx+zL33FsZWWUYKELnkBgeG8xAnmahlUpAPAo0u+B7d22 qWTNh/+zqQ3odTsnb16qFA9BWgp/BSsyg1H4NnRdQG0HDedPdmPAol/B/T7BCfkh1gCo s8G7V9f6lbrw8jZ1C5QykTyV+y5rLNCpgchMbNjVyVi3U7TrY5MWa8HiJwTF8KQ63nga inM9eAXcXr7g4pPUE8Drgldl+PGL8P8669wYqx/lgVtZwoMIwUS0xxCEumMTQFO/7d3w /EFg== MIME-Version: 1.0 X-Received: by 10.152.87.14 with SMTP id t14mr1896296laz.52.1394554595607; Tue, 11 Mar 2014 09:16:35 -0700 (PDT) Received: by 10.112.211.199 with HTTP; Tue, 11 Mar 2014 09:16:35 -0700 (PDT) In-Reply-To: <6e55ab$8gri5e@ironport10.mayo.edu> References: <042de8eb540ae1570118236295112e28@cs.wisc.edu> <6e55ab$8gqm9v@ironport10.mayo.edu> <6e55ab$8gri5e@ironport10.mayo.edu> Date: Tue, 11 Mar 2014 21:46:35 +0530 Message-ID: Subject: Re: How to use Drug NER From: ravi garg To: user@ctakes.apache.org Content-Type: multipart/alternative; boundary=001a11c34f224a893204f4570b75 X-Virus-Checked: Checked by ClamAV on apache.org --001a11c34f224a893204f4570b75 Content-Type: text/plain; charset=ISO-8859-1 Hey, Yes, It is populated with the medication. I was actually getting that before too but not the drug ner type system part.. Also when I browse the inner annotations of MedicationMention, I can finally see other annotations too like medicationFrequency, medicationRoute etc in the refsem typesystem. Thank you very much for the help. I would try to uncomment the code you are referring and try to rebuild that part.Just one final help can you please kindly point me to the code you are talking about. Thanks, Ravi On Tue, Mar 11, 2014 at 9:18 PM, Murphy, Sean P. wrote: > Ravi, > > Can you look at the list of IdentifiedAnnotation to see if > the entities include the drugs in question. Specifically, the > 'ctakes.typesystem.type.textsem.MedicationMention' should be populated. > Additionally, there should be the missing drug related annotations, such as > strength in that list. > > The problem is that the drug ner was migrated to use the > new type system a release or two back. However, the old type system format > was allowed to remain in the event that someone required that legacy > handling. These can actually be populated by uncommenting some code that > exists in the DrugMention source code and rerunning. > > I had forgotten about these changes. Hopefully, that > explains what you're seeing. > > Thanks, > > ~Sean > > > > *From:* ravi garg [mailto:ravigarg27@gmail.com] > *Sent:* Tuesday, March 11, 2014 10:15 AM > > *To:* user@ctakes.apache.org > *Subject:* Re: How to use Drug NER > > > > Hey, > > I am using > ctakes-drug-ner/desc/analysis_engine/AggregatePlainTextUMLSProcessor.xml as > the Analysis Engine in the CVD where in I am getting the other annotations > such as Medication Annotations Fraction Annotation which are of > ctakes.typesystem.type.textsem.IdentifiedAnnotation but do not get any of > the ctakes.drugner.type annotations for eg Frequency Annotation Drug > Strength Annotations etc. I dont get any errors though but I feel > DrugMentionAnnotator descriptor which extracts the strength, frequency, > route etc is not working for me. > > Thanks, > > Ravi > > > > On Tue, Mar 11, 2014 at 8:18 PM, Murphy, Sean P. > wrote: > > Ravi, > > I assume you're just using plain text as the input for the > pipeline. Did you use the provided sample DrugNER_PlainText_CPE.xml > available in the ctakes-drug-ner/desc/collection_processing_engine/ folder > to see if it can run the provided sample? > > If my assumption is correct than make sure you're using > the Analysis Engines provided for the plain text path (i.e. no aggregates > with 'CDA' in the name should be utilized). This also pertains to the > consumer which output ( make sure to use this one > 'AggregatePlaintextProcessor.xml'). > > If you are using the CVD (cas visual debugger) then > everything but the consumer would still apply. Just be sure that you are > loading the DrugAggregatePlaintextUMLSProcessor AE specifier. > > BTW. Are you seeing other annotations other than the > drugner type? > > > > Thanks, > > ~Sean > > > > *From:* ravi garg [mailto:ravigarg27@gmail.com] > *Sent:* Tuesday, March 11, 2014 2:38 AM > > > *To:* user@ctakes.apache.org > *Subject:* Re: How to use Drug NER > > > > Ohh Okay, I am sorry Sean, I didn't actually knew Rxnorm is an umls > dictionary and you need to have a license to use it. I have got that > working but still I dont get any annotations in drugner.type for example > RouteAnnotation, DurationAnnotation etc. Any ideas on how to get that > working > > Thanks, > > Ravi > > > > On Mon, Mar 10, 2014 at 11:56 PM, ravi garg wrote: > > Hey Xiayuan, > > I ensured that the directory of the resource that is the rxnorm_index is > correct and cTAKES is also actually using it. I can see the logs wherein > cTAKES actually parses 16k docs. I get no errors though on using the > pipeline but nothing is extracted or annotated. Even the dosage, frequency > and route which I believe are not dependent on drug dictionary are also not > getting identified. I have worked on the main clinical pipeline before but > am working on the Drug pipeline for the first time so no idea whats wrong. > > Regards, > > Ravi > > > > On Mon, Mar 10, 2014 at 11:38 PM, Xiayuan Huang > wrote: > > Hi Ravi, > > Currently I am doing one project using cTAKES. I am trying to use a > pipeline for identifying smoking status, SimulatedProdSmokingTAE.xml. And I > also encountered some problem on executing those pipelines. Some possible > errors will be the directory of UIMA resource, you have to set that > correctly. And I got some exceptions when I try to run pipelines. We can > discuss how to implement cTAKES later on, I guess I really need someone to > discuss and help out on this cTAKES system. > > Best, > Xiayuan Huang > > > > > On 2014-03-10 11:05, ravi garg wrote: > > Hey, > > I am using DrugAggregatePlainTextProcessor.xml as my analysis engine > annotator. I have downloaded all the required resources by cTAKES 3.1 > . I guess it uses the rxnorm_index as the drug database. But I am not > getting any annotations as the output. Please let me know the correct > way using Drug NER > > Thanks, > Ravi > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > > > > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > > > > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > > > > > -- > > Ravi Garg > 4th Year > MSc (hons) Biological Sciences > B.E (hons) Computer Science and Engineering > BITS Pilani KK Birla Goa Campus > -- Ravi Garg 4th Year MSc (hons) Biological Sciences B.E (hons) Computer Science and Engineering BITS Pilani KK Birla Goa Campus --001a11c34f224a893204f4570b75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hey,

Yes, It is populated with= the medication. I was actually getting that before too but not the drug ne= r type system part.. Also when I browse the inner annotations of Medication= Mention, I can finally see other annotations too like medicationFrequency, = medicationRoute etc in the refsem typesystem. Thank you very much for the h= elp. I would try to uncomment the code you are referring and try to rebuild= that part.Just one final help can you please kindly point me to the code y= ou are talking about.

Thanks,
Ravi

On Tue, Mar 11, 2014 at 9:18 PM, Murphy, Sean P= . <Murphy.Sean@mayo.edu> wrote:

Ravi,

    &= nbsp;           Can you l= ook at the list of IdentifiedAnnotation to see if the entities include the = drugs in question.   Specifically, the ‘ctakes.typesystem.t= ype.textsem.MedicationMention’ should be populated. Additionally, there should be the missing drug relate= d annotations, such as strength in that list.

    &= nbsp;           The probl= em is that the drug ner was migrated to use the new type system a release o= r two back.  However, the old type system format was allowed to remain in the event that someone required that legacy handling.  T= hese can actually be populated by uncommenting some code that exists in the= DrugMention source code and rerunning.

    &= nbsp;           I had for= gotten about these changes.  Hopefully, that explains what you’r= e seeing.

    &= nbsp;           Thanks,&n= bsp;            = ;  

    &= nbsp;            &nb= sp;            =   ~Sean

 

From: ravi gar= g [mailto:ravigar= g27@gmail.com]
Sent: Tuesday, March 11, 2014 10:15 AM


To: user= @ctakes.apache.org
Subject: Re: How to use Drug NER

 

Hey,

I am using ctakes-dru= g-ner/desc/analysis_engine/AggregatePlainTextUMLSProcessor.xml as the Analy= sis Engine in the CVD where in I am getting the other annotations such as M= edication Annotations Fraction Annotation which are of ctakes.typesystem.type.textsem.IdentifiedAnnotation but do no= t get any of the ctakes.drugner.type annotations for eg Frequency Annotatio= n Drug Strength Annotations etc. I dont get any errors though but I feel Dr= ugMentionAnnotator descriptor which extracts the strength, frequency, route etc is not working for me. =

Thanks,

Ravi

 <= /p>

On Tue, Mar 11, 2014 at 8:18 PM, Murphy, Sean P. <= ;Murphy.Sean@mayo= .edu> wrote:

Ravi,

    &= nbsp;           I assume = you’re just using plain text as the input for the pipeline.  Did= you use the provided sample DrugNER_PlainText_CPE.xml available in the ctakes-drug= -ner/desc/collection_processing_engine/ folder to see if it can run the pro= vided sample?

    &= nbsp;           If my ass= umption is correct than make sure you’re using the Analysis Engines p= rovided for the plain text path (i.e. no aggregates with ‘CDA’ in the = name should be utilized).  This also pertains to the consumer which ou= tput ( make sure to use this one ‘AggregatePlaintextProcessor.xml&rsq= uo;).

    &= nbsp;           If you ar= e using the CVD (cas visual debugger) then everything but the consumer woul= d still apply.   Just be sure that you are loading the DrugAggrega= tePlaintextUMLSProcessor AE specifier.

    &= nbsp;           BTW. = ; Are you seeing other annotations other than the drugner type?

    &= nbsp;          

    &= nbsp;           Thanks,

    &= nbsp;            &nb= sp;            =   ~Sean

 

From: ravi gar= g [mailto:ravigar= g27@gmail.com]
Sent: Tuesday, March 11, 2014 2:38 AM


To: user= @ctakes.apache.org
Subject: Re: How to use Drug NER

 

Ohh Okay, I am sorry = Sean, I didn't actually knew Rxnorm is an umls dictionary and you need = to have a license to use it. I have got that working but still I dont get a= ny annotations in drugner.type for example RouteAnnotation, DurationAnnotation etc. Any idea= s on how to get that working

Thanks,

Ravi

 <= /p>

On Mon, Mar 10, 2014 at 11:56 PM, ravi garg <ravigarg27@gmail.com<= /a>> wrote:

Hey Xiayuan,

I ensured that the di= rectory of the resource that is the rxnorm_index is correct and cTAKES is a= lso actually using it. I can see the logs wherein cTAKES actually parses 16= k docs. I get no errors though on using the pipeline but nothing is extracted or annotat= ed. Even the dosage, frequency and route which I believe are not dependent = on drug dictionary are also not getting identified. I have worked on the ma= in clinical pipeline before but am working on the Drug pipeline for the first time so no idea whats wrong.=

Regards,

Ravi

 <= /p>

On Mon, Mar 10, 2014 at 11:38 PM, Xiayuan Huang <= huangxy@cs.wisc.ed= u> wrote:

Hi Ravi,

Currently I am doing one project using cTAKES. I am trying to use a pipelin= e for identifying smoking status, SimulatedProdSmokingTAE.xml. And I also e= ncountered some problem on executing those pipelines. Some possible errors = will be the directory of UIMA resource, you have to set that correctly. And I got some exceptions when I try to ru= n pipelines. We can discuss how to implement cTAKES later on, I guess I rea= lly need someone to discuss and help out on this cTAKES system.

Best,
Xiayuan Huang




On 2014-03-10 11:05, ravi garg wrote:

Hey,

I am using DrugAggregatePlainTextProcessor.xml as my analysis engine
annotator. I have downloaded all the required resources by cTAKES 3.1
. I guess it uses the rxnorm_index as the drug database. But I am not
getting any annotations as the output. Please let me know the correct
way using Drug NER

Thanks,
Ravi

--

Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus




--

Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus




--

Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus




--

Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus




--
Ravi G= arg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Sc= ience and Engineering
BITS Pilani KK Birla Goa Campus
--001a11c34f224a893204f4570b75--