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 6CE87113A2 for ; Wed, 18 Jun 2014 14:12:22 +0000 (UTC) Received: (qmail 56654 invoked by uid 500); 18 Jun 2014 14:12:22 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 56615 invoked by uid 500); 18 Jun 2014 14:12:22 -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 56604 invoked by uid 99); 18 Jun 2014 14:12:21 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 18 Jun 2014 14:12:21 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (athena.apache.org: domain of vngarla@gmail.com designates 209.85.217.171 as permitted sender) Received: from [209.85.217.171] (HELO mail-lb0-f171.google.com) (209.85.217.171) by apache.org (qpsmtpd/0.29) with ESMTP; Wed, 18 Jun 2014 14:12:17 +0000 Received: by mail-lb0-f171.google.com with SMTP id s7so569597lbd.30 for ; Wed, 18 Jun 2014 07:11:55 -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=zSCi6wxcfyQpMCg36d1rd6kyWxDf9qix/NGKRCRA7r4=; b=0kBkznrlTqmHd92x/dQ4EfRX1OebBl8MYCw/VOMsfXMH3alVWw3UmThycR/B/YZlXP S194jdRZSd+IFAdwYi8VEc92hnZUw+M0Jakjy3Na/KV7akkK/J36DS18BK9uPE0LI3ZD rtj2XQ6uq/16rlHiztXpGLRc4jSuRg1+oYS1D9BfC6xXWv55D50CJGLYqHbB1lbeZQgC Flj63Tp+0ED0l5hnQpPtpT8g5Cs6tk+jeYJsWf9tzUftkLZkfWA1OiBcbWIGaLrCEb06 rc3kRVLoA9/6bl6oyv0a9gbsbv4/mmmxTw4ApCrpxKKmsVjAj2jGn+SZs0O6ZiEQV8fj VEJw== MIME-Version: 1.0 X-Received: by 10.152.43.8 with SMTP id s8mr1426381lal.81.1403100715383; Wed, 18 Jun 2014 07:11:55 -0700 (PDT) Received: by 10.153.4.164 with HTTP; Wed, 18 Jun 2014 07:11:55 -0700 (PDT) In-Reply-To: References: <924DE05C19409B438EB81DE683A942D91081808D@CHEXMBX1A.CHBOSTON.ORG> <924DE05C19409B438EB81DE683A942D9108183B2@CHEXMBX1A.CHBOSTON.ORG> Date: Wed, 18 Jun 2014 10:11:55 -0400 Message-ID: Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProcessor.xml From: vijay garla To: user@ctakes.apache.org Content-Type: multipart/alternative; boundary=001a11c23656b97fbd04fc1cd714 X-Virus-Checked: Checked by ClamAV on apache.org --001a11c23656b97fbd04fc1cd714 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable The YTEX AggregatePlaintextUMLSProcessor differs from the default AggregatePlaintextUMLSProcessor in the following a ways: * Use SegmentRegexAnnotator instead of SimpleSegmentAnnotator * Use SentenceDetectorAnnotator without splitting on newlines * Added SenseDisambiguatorAnnotator ** Use YTEX DictionaryLookupAnnotatorDB instead of cTAKES DictionaryLookupAnnotatorDB* The YTEX dictionary lookup is different from cTAKES': * uses the old dictionary lookup * uses a single dictionary * uses a single lookup consumer that creates plain-vanilla EntityMention annotations (none of the subtypes) I think that if you change the YTEX AggregatePlaintextUMLSProcessor to point at the cTAKES dictionary lookup, you will get approximately same annotations (probably more if sentences do not end on newlines, as dictionary lookup is not performed across sentences) could you try the following please: In desc\ctakes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.= xml change To And re-run. You should get the same results (keep in mind the newline thing). On Wed, Jun 18, 2014 at 9:46 AM, Lee, Richard A. [USA] wrote: > Yes, that exactly the problem I=E2=80=99ve been reporting. I think you= =E2=80=99ll see > that it you still get the non-Medical annotations, like Date, RomanNumera= l, > et al, but not DiseaseDisorderMention and the other Medical ones, right? > > > > I=E2=80=99m still hoping someone can assist with this. > > > > *From:* Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in] > *Sent:* Wed, 18 Jun, 2014 04:43 > *To:* user@ctakes.apache.org > *Subject:* Re: [External] Re: Cannot load > AggregatePlainTextUmlsProcessor.xml > > > > Found a fix. Will post it here in case it helps someone. When using > ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml from " > CTAKES_HOME/desc/ytex-uima/desc/analysis_engine/ > AggregatePlaintextUMLSProcessor.xml" and not from the usual " > CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/ > AggregatePlaintextUMLSProcessor.xml" as given here > . > > However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLS= Processor.xml" > produced even less annotations than " > ctakes-clinical-pipeline/desc/analysis_engine/ > AggregatePlaintextUMLSProcessor.xml". > > I expected ytex-specific AE to produce better results. But clearly that's > not the case. > > > > On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj > wrote: > > Hi. Thanks for the reply. > I have a file named LookupDesc_Db.xml which has the line tableName=3D"@db.schema@.v_snomed_fword_lookup"/> > > instead of LookupDesc_SNOMED.*template*.xml. Also, my ytex.properties > file seems fine. I have attached the file for your reference. > And yes, when running the ant setup by following #7 on this > li= nk, > it sends the output to "setup.out". The build was successful though. I > didn't see any errors. I am attaching the file for your reference as well= . > Please have a look and let me know. > > > --001a11c23656b97fbd04fc1cd714 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
The YTEX AggregatePlaintextUMLSProcessor differs from the = default AggregatePlaintextUMLSProcessor in the following a ways:
* Use S= egmentRegexAnnotator instead of SimpleSegmentAnnotator
* Use SentenceDet= ectorAnnotator without splitting on newlines
* Added SenseDisambiguatorAnnotator
* Use YTEX DictionaryLookupAnnota= torDB instead of cTAKES DictionaryLookupAnnotatorDB

= The YTEX dictionary lookup is different from cTAKES':
* uses = the old dictionary lookup
* uses a single dictionary
* uses a single lookup consumer t= hat creates plain-vanilla=C2=A0EntityMention annotations (none of the subty= pes)

I think that if you change the YTEX Aggregate= PlaintextUMLSProcessor to point at the cTAKES dictionary lookup, you will g= et approximately same annotations (probably more if sentences do not end on= newlines, as dictionary lookup is not performed across sentences)

could you try the following please:
In desc\c= takes-ytex-uima\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml ch= ange
<= ;delegateAnalysisEngine key=3D"DictionaryLookupAnnotatorDB">
<import locati= on=3D"./DictionaryLookupAnnotator.xml" />
</delegateAnalysisEngine>
To
=C2=A0 =C2=A0 <delegateAnalysisEngine key=3D"= ;DictionaryLookupAnnotatorDB">
=C2=A0 =C2=A0 =C2=A0 <i= mport location=3D"../../../ctakes-dictionary-lookup/desc/analysis_engi= ne/DictionaryLookupAnnotatorUMLS.xml"/>
=C2=A0 =C2=A0 </delegateAnalysisEngine>

And re-run. =C2=A0You should get the same results (keep in mind the = newline thing).





On Wed, Jun 1= 8, 2014 at 9:46 AM, Lee, Richard A. [USA] <lee_richard@bah.com> wrote:

Yes, that exactly the problem I=E2=80=99ve b= een reporting. I think you=E2=80=99ll see that it you still get the non-Med= ical annotations, like Date, RomanNumeral, et al, but not DiseaseDisorderMention and the other Medical ones, right?

=C2=A0

I=E2=80=99m still hoping someone can assist = with this.

=C2=A0

From: Abhishek Raj [mailto:abhishekrm@iitrpr.ac.in]
Sent: Wed, 18 Jun, 2014 04:43
To: user= @ctakes.apache.org
Subject: Re: [External] Re: Cannot load AggregatePlainTextUmlsProces= sor.xml

=C2=A0

Found a fix. Will post it here in case it helps some= one. When using ctakes-3.1.2, load the AggregatePlainTextUmlsProcessor.xml = from "CTAKES_= HOME/desc/ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml<= /span>" and not from the usual "CTAKES_HOME/desc/ctakes-clinical-pipeline/desc/analysis_engine/= Ag= gregatePlaintextUMLSProcessor.xml" as given here.

However strangely, "ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml&quo= t; prod= uced even less anno= tations than "ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintext= UMLSProcessor.xml".

I expected ytex-specific AE to produce better results. But clearly tha= t's not the case.

=C2=A0

On Thu, Jun 12, 2014 at 2:51 AM, Abhishek Raj <abhishekrm@iitrp= r.ac.in> wrote:

Hi. Thanks for the reply.
I have a file named=C2=A0LookupDesc_Db.xml which has the line=C2=A0<jdbcImpl tableName= =3D"@db.schema@.v_snomed_fword_lookup"/><= /p>

instead of=C2=A0LookupDesc_SNOMED.template.xml. Also, my yte= x.properties file seems fine. I have attached the file for your reference.<= br> And yes, when running the ant setup by following #7 on=C2=A0this=C2=A0link, it sends the output to "setup.out= ". The build was successful though. I didn't see any errors. I am attaching the file for your reference as well. Please have a = look and let me know.

=C2=A0


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