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From: "Masanz, James J." <Masanz.James@mayo.edu>
To: "'ctakes-user@incubator.apache.org'"
 <ctakes-user@incubator.apache.org>
Subject: RE: Regarding Assertion Tagger
Thread-Topic: Regarding Assertion Tagger
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Date: Mon, 3 Dec 2012 21:30:05 +0000
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Hi Deepal,

If by question #3, you are looking for a way to get a mapping from a cTAKES=
 annotation to the semantic type for the concept, this is already done with=
in cTAKES (for the following 4 groupings: Diseases/disorders, Signs/symptom=
s, Procedures, Anatomical sites)
FYI, These groupings are based on the lists of TUIs within the LookupDesc*.=
xml files within cTAKES.
The concept (aka clinical named entity) annotations created by cTAKES are l=
inked to UmlsConcept annotations, which contain an attribute called tui.
>From the TUI (such as T047) you can map to the textual name of the semantic=
 type such as "Disease or Syndrome"

See the annotations of type UmlsConcept that are produced by cTAKES, which =
include the CUI and the TUI, and you can map to the list of semantic type n=
ames from this table:
http://semanticnetwork.nlm.nih.gov/Download/RelationalFiles/SRDEF

For example, if cTAKES annotates "AIDS",  there will be a UmlsConcept annot=
ation with cui=3D"C0011884" tui=3D"T047", where T047 is the TUI for "Diseas=
e or Syndrome"

Regards,=20
James Masanz

From: ctakes-user-return-37-Masanz.James=3Dmayo.edu@incubator.apache.org [m=
ailto:ctakes-user-return-37-Masanz.James=3Dmayo.edu@incubator.apache.org] O=
n Behalf Of Murphy, Sean P.
Sent: Friday, November 30, 2012 8:58 AM
To: 'Deepal Dhariwal'; ctakes-dev@incubator.apache.org
Cc: <ctakes-user@incubator.apache.org>
Subject: RE: Regarding Assertion Tagger

Deepal,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Thanks for verifying #1.=A0=A0 I=
t took a bit longer to setup my environment on a test machine to verify, bu=
t please bear with me while I run through a regime of tests regarding these=
 pipelines.=A0 =A0=A0

#2. You may need to increase the pool size used by the VM arguments for you=
r java environment.=A0 I believe the default is " -Xms1024M -Xmx2048M".=A0=
=A0 If your system has the resources you may want to increase these by 1GM =
and retest.=A0 I do not believe this will improve the time to run, however.=
=A0=A0=A0 Perhaps someone else has some suggestions regarding this aspect(?=
).

#3.=A0 I will have to defer this question to the rest of the team.


From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]=20
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org
Cc: Murphy, Sean P.; <ctakes-user@incubator.apache.org>
Subject: Re: Regarding Assertion Tagger

Hello all,

1. I downloaded ctakes 3.0 and was trying the PAD term Spotter and Drug NER=
 lookup annotator, but I am getting Resource Initialization Exception.I hav=
e valid UMLS license and I have added username , password in UMLS Lookup An=
notator. =A0 I have been following the thread on PAD Term Spotter bug in ct=
akes 2.5 and I wanted to know whether it has been resolved in ctakes 3.0
2. Further my input data set is 4 MB. When I run Collection Processing Engi=
ne on the data set I get java.lang.outofmemory java heap space exception. I=
s there any way I could resolve this error and also reduce the time taken t=
o execute on such huge data set.
3. Lastly as part of my thesis I am working on extracting cardio vascular t=
erms from medical text using ctakes and umls vocabulary. I want to map thes=
e terms to existing medical owl ontologies for example, UMLS Semantic Netwo=
rk. I wanted to know whether ctakes community is thinking including medical=
 ontology feature in ctakes.

Thanks
Deepal Dhariwal


On Mon, Nov 26, 2012 at 12:25 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu=
> wrote:
Thanks Sean,
If the issue was just a descriptor path issue, then it was probably already=
 fixed in 3.0 as part of the ASF move.
We can just verify and test it?

--Pei

> -----Original Message-----
> From: Murphy, Sean P. [mailto:Murphy.Sean@mayo.edu]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: ctakes-dev@incubator.apache.org; <ctakes-user@incubator.apache.org>
> Subject: RE: Regarding Assertion Tagger
>
> Hello Pei,
> =A0 =A0 =A0 I have created a bug for the 3.0 branch as well. =A0 However,=
 since the
> problem is related to the relative path structures being incorrectly migr=
ated
> to the updated format, =A0I am not sure if the fix should be made to the
> sourceforge 2.5 version only or all releases. =A0 =A0The maven driven bui=
ld changes
> appear to be consolidating some of these issues, but won't be in place un=
til
> the 3.0 build has finalized. =A0 =A0If so, and please correct me if I'm w=
rong, then:
> =A0 =A0 =A0 1) There is no need to fix at 2.6. and
> =A0 =A0 =A0 2) The fix checked in at 3.0 would be the based on the old di=
rectory
> structure.
> =A0 =A0 =A0 Thanks,
> =A0 =A0 =A0 =A0 =A0 =A0 =A0 ~Sean
>
> -----Original Message-----
> From: ctakes-user-return-31-
> Murphy.Sean=3Dmayo.edu@incubator.apache.org [mailto:ctakes-user-return-
> 31-Murphy.Sean=3Dmayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ctakes-user@incubator.apache.org>
> Cc: <ctakes-user@incubator.apache.org>; ctakes-dev@incubator.apache.org
> Subject: Re: Regarding Assertion Tagger
>
> There's a 3.0.0 branch. =A0The release will be made from there. =A0So we =
should
> make the fixes in both trunk and 3.0.0.
>
>
> On Nov 15, 2012, at 10:32 PM, "Murphy, Sean P."
> <Murphy.Sean@mayo.edu> wrote:
>
> > Hello Pei,
> > =A0 =A0The issue is at 2.5. =A0 When is the 3.0 release freeze? =A0 I w=
ill try to propagate
> the fix forward.
> >
> > -----Original Message-----
> > From: ctakes-user-return-29-
> Murphy.Sean=3Dmayo.edu@incubator.apache.org
> > [mailto:ctakes-user-return-29-
> Murphy.Sean=3Dmayo.edu@incubator.apache.or
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ctakes-user@incubator.apache.org>
> > Cc: ctakes-user@incubator.apache.org; ctakes-dev@incubator.apache.org
> > Subject: Re: Regarding Assertion Tagger
> >
> > Hi Sean,
> > What was the issue in 2.5? =A0Just want to make sure this is also fixed=
 in the
> upcoming 3.0 release coming out of ASF as well... Jira#?
> >
> >
> >
> > On Nov 15, 2012, at 7:59 PM, "Murphy, Sean P."
> <Murphy.Sean@mayo.edu> wrote:
> >
> >> I was able to see an issue with the 'PAD term spotter' which will most
> likely be related to the problem you're seeing with the smoking status as
> well. =A0 =A0The problem seems to have =A0stemmed from the reorganization=
 of the
> path structures with the latest cTAKES =A0release. =A0Due to time and res=
ource
> constraints we were not able to test each project independently.
> >>
> >> I will open a bug report against these problems and provide a fix as s=
oon
> as possible. =A0I will keep you posted, but I hope to have this resolved =
in a few
> days.
> >> =A0 Thanks,
> >> =A0 =A0 =A0 ~Sean
> >>
> >> -----Original Message-----
> >> From: ctakes-user-return-26-
> Murphy.Sean=3Dmayo.edu@incubator.apache.org
> >> [mailto:ctakes-user-return-26-
> Murphy.Sean=3Dmayo.edu@incubator.apache.o
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Cc: ctakes-user@incubator.apache.org
> >> Subject: Re: Regarding Assertion Tagger
> >>
> >> You were looking in the right place Deepal! The "cTAKES 2.5 Component
> Use Guide" (the link at the bottom of your email) has a link to more
> information about the assertion module.
> >>
> >> Assertion module info:
> >>
> >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Assertion
> >>
> >> I'm not familiar with the peripheral artery disease spotter or the sim=
ulated
> prod smoking tae. =A0So I'll let someone else chime in there.
> >>
> >> Matt
> >>
> >>
> >> On 2012-11-15 13:11 , "Deepal Dhariwal" <deepaldhariwal@gmail.com>
> wrote:
> >>
> >>> Hello Matt,
> >>>
> >>> Thanks for your reply. I am using cTAKES-2.5.0 Binary Version which
> >>> I have downloaded from
> >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+User+Install+Instruc
> >>> t
> >>> io
> >>> ns
> >>> .
> >>> I have gone through the cTAKES documentation however no where was
> it
> >>> mentioned that polarity / uncertainty properties are on Entity Mentio=
n.
> >>> In order to avoid sending repeated mails to the mailing list could
> >>> you tell me if there is some other documentation as well ? I am
> >>> trying to use Peripheral Artery Disease Spotter , however it returns
> >>> only document annotation. Further even the SimulatedProdSmokingTAE
> >>> Annotator returns smoking status 'unknown' for every input. Is there
> >>> some order in which these annotator need to be executed (Reference :
> >>>
> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+Component+Use+Guide
> >>> )
> >>>
> >>> Thanks for clarifying the user list email id.
> >>>
> >>> Regards
> >>> Deepal Dhariwal
> >>>
> >>> On Thu, Nov 15, 2012 at 12:48 PM, Coarr, Matt <mcoarr@mitre.org>
> wrote:
> >>>
> >>>> FYI, the user list is ctakes-user (singular). =A0I've corrected the =
CC.
> >>>>
> >>>> The polarity/conditional/uncertainty properties are on
> >>>> EntityMention and EventMention.
> >>>>
> >>>> Are you using a current development copy of ctakes (from apache svn
> >>>> or from 3.0 RC2)?
> >>>>
> >>>> If not, what version of ctakes are you using? =A0Version number?
> >>>> Binary, source zip, or source from svn?
> >>>>
> >>>> Matt
> >>>>
> >>>>
> >>