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 B403611C0F for ; Sat, 24 May 2014 00:07:58 +0000 (UTC) Received: (qmail 12344 invoked by uid 500); 24 May 2014 00:07:58 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 12311 invoked by uid 500); 24 May 2014 00:07:58 -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 12304 invoked by uid 99); 24 May 2014 00:07:58 -0000 Received: from Unknown (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 24 May 2014 00:07:58 +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 (nike.apache.org: domain of vngarla@gmail.com designates 209.85.217.182 as permitted sender) Received: from [209.85.217.182] (HELO mail-lb0-f182.google.com) (209.85.217.182) by apache.org (qpsmtpd/0.29) with ESMTP; Sat, 24 May 2014 00:07:55 +0000 Received: by mail-lb0-f182.google.com with SMTP id z11so3180239lbi.13 for ; Fri, 23 May 2014 17:07:32 -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=FwyAsuP0ffFFGOaAtQC2Gdvv2tQRB8IZXF68+s+IbM0=; b=Ms+xjfIzrxAteymv/MfYrdS9NCtNI6rVwW+4ctnVCMhWju5QlL3lR/AucTtJeCbpYq EENokn6gQkv3i5ZjgCs69rXyBRSMkj4728KLxHZjToWZdkhXE2wA0RN7NRlaRnWYQUIA bvxyYQkzmqbZqxTTqbxki4MDl6UpcT4jgE0xNSa7cXVdr2DjwR1Vaf+ZBSDkx8UxD0cp K94lLgdj2asOPg2AjPpnx2al3yJT8z0bIZN/mpe2uOIyj7Ac07HvAqQmbZXRaSU3fiLz ZoW2yJ7UvSrcYUkBu6GZdKuvNV8yasFMy8/U7FLg5kMarp+AWZtfvqcDxV5nbEyBDmx3 aOnA== MIME-Version: 1.0 X-Received: by 10.152.121.39 with SMTP id lh7mr5591474lab.7.1400890051904; Fri, 23 May 2014 17:07:31 -0700 (PDT) Received: by 10.152.43.169 with HTTP; Fri, 23 May 2014 17:07:31 -0700 (PDT) In-Reply-To: References: Date: Fri, 23 May 2014 20:07:31 -0400 Message-ID: Subject: Re: ctakes 3.1.2 produces no medical annotations for me From: vijay garla To: user@ctakes.apache.org Content-Type: multipart/alternative; boundary=089e01177487e9c94804fa1a2114 X-Virus-Checked: Checked by ClamAV on apache.org --089e01177487e9c94804fa1a2114 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Richard, Did you add SNOMED-CT when creating your UMLS Subset? The dictionary that YTEX ships with has ~1.5 million entries. If that doesn't work, you can also try running the stock cTAKES AggregatePlaintextUMLSProcessor to see if that creates different annotations. HTH, -vj On Fri, May 23, 2014 at 4:58 PM, Lee, Richard A. [USA] wrote: > Hi, folks. > > > > I=E2=80=99ve been trying to use the new cTAKES 3.1.2 with ytex, using the > AggregatePlaintextUMLSProcessor.xml AE under ctakes-ytex-uima, and so far > it=E2=80=99s not been producing the numerous medical annotations (eg > DiseaseDisorderMention) that I was getting on the same documents with > cTAKES 3.1.1. Attached screenshot will hopefully make this clear. > > > > I did use MetamorphoSys to set up the UMLS tables, and then the ytex > script to populate its schema, and I now have ytex tables with hundreds o= f > thousands of entries. > > > > I=E2=80=99ve upped the logging level in the hopes the log file would prov= ide a > clue, and the only thing I=E2=80=99m seeing is a lot of =E2=80=9CDEBUG > [FirstTokenPermutationImpl] Window size of 8 exceeds the max permutation > level of 7.=E2=80=9D; that number varies from 8 to 12. > > > > Would that explain the problem? If so, how do I fix it? If not, how do I > find the problem? Thanks. > > > > > --089e01177487e9c94804fa1a2114 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Richard,

Did you add SNOMED-CT when = creating your UMLS Subset? =C2=A0The dictionary that YTEX ships with has ~1= .5 million entries. =C2=A0If that doesn't work, you can also try runnin= g the stock cTAKES=C2=A0AggregatePlaintextUMLSProcessor to see= if that creates different annotations. =C2=A0

HTH,

-vj

<= br>
On Fri, May 23, 2014 at 4:58 PM, Lee, Richard= A. [USA] <lee_richard@bah.com> wrote:

Hi, folks.

=C2=A0

I=E2=80=99ve been trying to use the new cTAKES 3.1.2= with ytex, using the AggregatePlaintextUMLSProcessor.xml AE under ctakes-y= tex-uima, and so far it=E2=80=99s not been producing the numerous medical a= nnotations (eg DiseaseDisorderMention) that I was getting on the same documents with cTAKES 3.1.1. Attached screenshot will = hopefully make this clear.

=C2=A0

I did use MetamorphoSys to set up the UMLS tables, a= nd then the ytex script to populate its schema, and I now have ytex tables = with hundreds of thousands of entries.

=C2=A0

I=E2=80=99ve upped the logging level in the hopes th= e log file would provide a clue, and the only thing I=E2=80=99m seeing is a= lot of =E2=80=9CDEBUG [FirstTokenPermutationImpl] Window size of 8 exceeds= the max permutation level of 7.=E2=80=9D; that number varies from 8 to 12.

=C2=A0

Would that explain the problem? If so, how do I fix = it? If not, how do I find the problem? Thanks.

=C2=A0

=C2=A0


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