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 6729210580 for ; Tue, 11 Mar 2014 14:49:31 +0000 (UTC) Received: (qmail 30768 invoked by uid 500); 11 Mar 2014 14:49:30 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 30647 invoked by uid 500); 11 Mar 2014 14:49:25 -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 30622 invoked by uid 99); 11 Mar 2014 14:49:24 -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 14:49:24 +0000 X-ASF-Spam-Status: No, hits=-0.1 required=5.0 tests=HTML_MESSAGE,MSGID_FROM_MTA_HEADER,RCVD_IN_DNSWL_MED,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: local policy) Received: from [129.176.212.47] (HELO mail10.mayo.edu) (129.176.212.47) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 11 Mar 2014 14:49:20 +0000 Received: from unknown (HELO mail10.mayo.edu) ([10.146.65.138]) by ironport10-dlp.mayo.edu with ESMTP; 11 Mar 2014 09:49:00 -0500 Message-Id: <6e55ab$8gqm9v@ironport10.mayo.edu> X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AvEEACciH1MKgMjM/2dsb2JhbABagkJ/wg2BNHSCJQEBAQQtEEwCAQgNBAQBASgHISUJCAIEE4dlAxbKQA1XhX+MXIIdAYJ9gTsEllcBiGGFcYh1 Received: from unknown (HELO msgoms04.mayo.edu) ([10.128.200.204]) by ironport10.mayo.edu with ESMTP; 11 Mar 2014 09:48:50 -0500 Date: Tue, 11 Mar 2014 14:48:47 +0000 From: "Murphy, Sean P." Subject: RE: How to use Drug NER In-reply-to: To: "user@ctakes.apache.org" MIME-version: 1.0 Content-type: multipart/alternative; boundary=_000_38DD5510DD255845934ABD523985843B0B989FE1MSGPEXCEI11Amfa_ Content-language: en-US Accept-Language: en-US Thread-topic: How to use Drug NER Thread-index: AQHPPHqm/SqG7DXeS0m9dl2K5PT86Jra8myAgAAE94CAAN0RgIAAIamw X-MS-Has-Attach: X-MS-TNEF-Correlator: References: <042de8eb540ae1570118236295112e28@cs.wisc.edu> X-CFilter-Loop: Reflected X-Virus-Checked: Checked by ClamAV on apache.org --_000_38DD5510DD255845934ABD523985843B0B989FE1MSGPEXCEI11Amfa_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable 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 availa= ble 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 everyth= ing 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 drugn= er 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 diction= ary and you need to have a license to use it. I have got that working but s= till 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 co= rrect and cTAKES is also actually using it. I can see the logs wherein cTAK= ES actually parses 16k docs. I get no errors though on using the pipeline b= ut nothing is extracted or annotated. Even the dosage, frequency and route = which I believe are not dependent on drug dictionary are also not getting i= dentified. I have worked on the main clinical pipeline before but am workin= g 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 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 run pipelines. We can discuss how to i= mplement 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 --_000_38DD5510DD255845934ABD523985843B0B989FE1MSGPEXCEI11Amfa_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

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 provided 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 output ( make sure to use this one ‘AggregatePlaintextProcessor= .xml’).

    &= 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 DrugAggreg= atePlaintextUMLSProcessor AE specifier.

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

    &= nbsp;          

    &= nbsp;           Thanks,

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

 <= /p>

From: ravi gar= g [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 h= ave a license to use it. I have got that working but still I dont get any a= nnotations in drugner.type for example RouteAnnotation, DurationAnnotation etc. Any ideas on how to get that work= ing

Thanks,

Ravi

 

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 annotated. Even the dosage, frequ= ency and route which I believe are not dependent on drug dictionary are als= o not getting identified. I have worked on the main clinical pipeline befor= e 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 <= 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

--_000_38DD5510DD255845934ABD523985843B0B989FE1MSGPEXCEI11Amfa_--