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Posted to dev@ctakes.apache.org by vijay garla <vn...@gmail.com> on 2014/02/05 23:33:15 UTC
Re: YTEX cTAKES 3.1.1 ready
Hi Vlad,
sorry that the instructions aren't clear.
re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot as
usual (this is unchanged from 3.1.1). After that you still have to apply
the lib and resources (these are things that cannot be distributed via
apache).
re 2) Yes, I need to update those docs. Hopefully will get to that at some
point. However, I assume you already have a UMLS DB (also assume SQL
Server). If you can't/don't want to use your existing umls DB, please tell
me. The I'll priortize upgrading the doc on importing the umls tables (the
scripts are there).
best,
VJ
On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> Hi VJ-
>
> so, with trial and error were able to make the distribution and now have
> the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
>
> Here's what's unclear.
>
> 1. Is now this the only (combined) thing that you need for ctakes 3.1.1 +
> Ytex?
> the current documentation (https://code.google.com/p/yte
> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> lation_cTAKES_3_1)
> which most probably is outdated, talks about installing cTakes 3.1.1 first
> and then applying 2 SNAPSHOT archives (downloadable) , lib and resources.
> This is a confusion point.
>
> 2. The directions to import UMLS subset are then outdated as well. Maybe
> one should use the old version (ctakes 2.5 and ytex 0.8) to
> import the RRF files for the UMLS subset and then just use the resulting
> db. Thoughts?
>
> Thanks,
> Vlad Valtchinov
> Brigham Rad
>
>
> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
>
>> Hi Vlad,
>>
>>
> All of ytex has been moved into ctakes, it is currently in a branch (
>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't have
>> to install ytex-0.8 - instead you will have to build and install from the
>> ytex branch to create your own distribution. Steps 2 & 3 are correct.
>>
>> Although it is a pain, if you have the jdk, maven, and svn, you can
>> easily build your own distro:
>> * open a command prompt
>> * make sure jdk, maven, and svn are in your path
>> * cd to some directory where you want to check stuff out (I like c:\temp)
>> * run the following commands
>> rmdir /s /q ctakes
>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
>> cd ctakes
>> mvn clean install -DskipTests
>>
>> And you will have the ctakes (with ytex) distro in
>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.zip
>>
>> What is the process for getting the ytex branch merged into trunk? As I
>> mentioned, there are very few changes to other ctakes classes/types - this
>> should be completely complementary and not affect any existing ctakes
>> functionality.
>>
>> -vj
>>
>>
>>
>>
>>
>>
>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
>>
>>> Hi VJ--
>>>
>>> this is great!! Thanks for all the hard work on it!
>>>
>>> We're starting to look into the new install. For now we're trying the
>>> binaries out.
>>>
>>> There were these questions about the proper install steps:
>>>
>>> 1. Do we first install ytex-0.8
>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
>>> SNAPSHOT lib and resources zips
>>> 3. Work our way to install the UMLS ontologies in the db
>>>
>>> Its is not entirely clear from the new document (
>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
>>> if there's still need to install ytex-0.8, or YTEX has been entirely
>>> merged into cTakes?
>>>
>>> If the last statement is correct, there are missing parts in i.e the
>>> UMLS install steps that are linked from the new ctakes 3.1.1 document.
>>>
>>> Thanks,
>>> vlad
>>>
>>>
>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
>>>>
>>>> Hello All,
>>>>
>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
>>>> Most of the YTEX functionality has been ported and integrated with cTAKES,
>>>> and I've tested with MySQL and MS SQL Server (oracle tests pending).
>>>>
>>>> Most of the changes were made in new projects - very little existing
>>>> cTAKES code has been modified. The only non-trivial changes are
>>>> in /ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api
>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
>>>> SingleDocumentProcessorCtakes to deal with newlines within sentences
>>>> correctly. Can somebody take a look at the changes in the ytex branch?
>>>>
>>>> I believe that the branch https://svn.apache.org/
>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes
>>>> trunk, but would like other users to test it as well. Questions:
>>>>
>>>> * How can I distribute the ctakes binary distribution to ytex users
>>>> before the merge? Can we make the branch build available somewhere? The
>>>> binary distribution is too large to host on the ytex google code site (max
>>>> 200 MB)
>>>> * Non-ASF libraries - I have segregated these out into their own zip
>>>> file that can be distributed via sourceforge. As a stopgap, I can upload
>>>> this to the ytex google code site, but would prefer to upload to
>>>> sourceforge.
>>>> * UMLS Derivatives - Ditto for these - would like to move to
>>>> sourceforge.
>>>> * Documentation - How can I update the confluence docs? I would
>>>> migrate the documentation from the google code website.
>>>>
>>>> Here the installation instructions (putting the wagon in front of the
>>>> horse ...)
>>>>
>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
>>>> ts=1388793998&updated=Installation_cTAKES_3_1
>>>>
>>>> Best,
>>>>
>>>> VJ
>>>>
>>>>
>>>> --
>>> You received this message because you are subscribed to the Google
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>>> To view this discussion on the web visit https://groups.google.com/d/
>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%40googlegroups.com
>>> .
>>>
>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>
>>
>> --
> You received this message because you are subscribed to the Google Groups
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>
> For more options, visit https://groups.google.com/groups/opt_out.
>
Re: YTEX cTAKES 3.1.1 ready
Posted by John Green <jo...@gmail.com>.
Completely non-contributory, but it is odd/humorous to see the headaches
that quickly written notes we do in the 5 minutes post-encounter lead to in
free-text analysis.
JG
On Thu, Feb 6, 2014 at 1:27 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Right, got it. I just wanted to let you know that some EMR notes -do-
> require sentence splitting at newline characters.
>
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Thursday, February 06, 2014 1:06 PM
> To: dev@ctakes.apache.org
> Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> vlad.valtchinov@gmail.com
> Subject: Re: YTEX cTAKES 3.1.1 ready
>
> The cTAKES sentence detector is not changed in the YTEX branch. The YTEX
> branch has an *additional* sentence detector that does not automatically
> split sentences on newlines - users can use this if they like.
>
> -vj
>
>
> On Thu, Feb 6, 2014 at 1:01 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi Vijay,
> >
> > > I have yet to run across clinical text from a real EMR where
> > > newlines
> > represent the end of a sentence
> >
> > Since James pointed out this possibility a couple weeks ago, I have
> > kept my eyes open. The problem is pretty ubiquitous in a corpus that
> > I'm working with right now. I just opened the first note and gave it
> > a count ... 95 lines total, 9 are sentence/phrase (lacking punctuation)
> endings.
> > This is not including lists, which comprise about half of the note.
> > One possible conjoinment was "Will consider [...] biopsy\nGiven [...]".
> > Depending upon how cTakes deals with it, the meaning could change
> > drastically.
> >
> > > I believe cTAKES absolutely has to support sentences with newlines
> > within them
> >
> > Yes, cTakes should do so, but I hope that you aren't suggesting that
> > it only support such a structure.
> >
> > Where is that easy button?
> >
> > -----Original Message-----
> > From: vijay garla [mailto:vngarla@gmail.com]
> > Sent: Thursday, February 06, 2014 10:31 AM
> > To: dev@ctakes.apache.org
> > Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > vlad.valtchinov@gmail.com
> > Subject: Re: YTEX cTAKES 3.1.1 ready
> >
> > I believe it is worth migrating to trunk.
> >
> > Note that the sentence detector is also complementary - the existing
> > ctakes sentence detector is unchanged - users can choose which
> > sentence detector to use. There are changes to assertion & dependency
> > parsing to support sentences without newlines, and that works with
> > both sentence detectors.
> >
> > I believe cTAKES absolutely has to support sentences with newlines
> > within them - I have yet to run across clinical text from a real EMR
> > where newlines represent the end of a sentence - the changes to
> > assertion & dependency parsing will have to be done at some point.
> >
> > -vj
> >
> >
> > On Thu, Feb 6, 2014 at 10:19 AM, Chen, Pei
> > <Pe...@childrens.harvard.edu>wrote:
> >
> > > VJ,
> > > Aside from the changes to the existing cTAKES code (sentence
> > > detector,
> > > etc.) [which we could leave out if it's still being debated], Do you
> > > think it's worth migrating the ytex code to trunk at this point?
> > > As you mentioned earlier, it's largely complementary.
> > > [I was just thinking of saving effort to maintain the separate
> > > branch and for simplicity for dev...]
> > >
> > > --Pei
> > >
> > > > -----Original Message-----
> > > > From: vijay garla [mailto:vngarla@gmail.com]
> > > > Sent: Wednesday, February 05, 2014 9:30 PM
> > > > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > > > vlad.valtchinov@gmail.com
> > > > Subject: Re: YTEX cTAKES 3.1.1 ready
> > > >
> > > > Hi Vlad,
> > > >
> > > > I Updated the umls install guide; see
> > > > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> > > >
> > > > I would prefer to add the docs in the ctakes confluence, but as
> > > > far as I
> > > can
> > > > tell, I don't have write access there - can somebody give me write
> > > privileges
> > > > on the ctakes confluence site?
> > > >
> > > > There was a bug in the umls install; copy
> > > > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> > > > ytex/scripts/data/build.xmlover
> > > > the corresponding file in your ctakes-3.1.2 install
> > > > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set.
> > > > The import is currently running on the UMLS 2013AA (I assume this
> > > > will
> > > complete
> > > > without issues as long as the umls schema hasn't changed from 2012).
> > > >
> > > > what trial and error did you have to go through to build the distro?
> > > >
> > > > -vj
> > > >
> > > >
> > > > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com>
> wrote:
> > > >
> > > > > Hi Vlad,
> > > > >
> > > > > sorry that the instructions aren't clear.
> > > > >
> > > > > re 1) What I am trying to say is install
> > > > > apache-ctakes-3.2.0-snapshot as usual (this is unchanged from
> > > > > 3.1.1). After that you still have to apply the lib and
> > > > > resources (these are things that cannot be distributed via apache).
> > > > >
> > > > > re 2) Yes, I need to update those docs. Hopefully will get to
> > > > > that at some point. However, I assume you already have a UMLS
> > > > > DB (also assume SQL Server). If you can't/don't want to use
> > > > > your existing umls DB, please tell me. The I'll priortize
> > > > > upgrading the doc on importing the umls tables (the scripts are
> there).
> > > > >
> > > > > best,
> > > > >
> > > > > VJ
> > > > >
> > > > >
> > > > > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> > > > >
> > > > >> Hi VJ-
> > > > >>
> > > > >> so, with trial and error were able to make the distribution and
> > > > >> now have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> > > > >>
> > > > >> Here's what's unclear.
> > > > >>
> > > > >> 1. Is now this the only (combined) thing that you need for
> > > > >> ctakes
> > > > >> 3.1.1 + Ytex?
> > > > >> the current documentation (https://code.google.com/p/yte
> > > > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> > > > >> lation_cTAKES_3_1)
> > > > >> which most probably is outdated, talks about installing cTakes
> > > > >> 3.1.1 first and then applying 2 SNAPSHOT archives
> > > > >> (downloadable) , lib and resources.
> > > > >> This is a confusion point.
> > > > >>
> > > > >> 2. The directions to import UMLS subset are then outdated as well.
> > > > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8)
> > > > >> to import the RRF files for the UMLS subset and then just use
> > > > >> the resulting db. Thoughts?
> > > > >>
> > > > >> Thanks,
> > > > >> Vlad Valtchinov
> > > > >> Brigham Rad
> > > > >>
> > > > >>
> > > > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> > > > >>
> > > > >>> Hi Vlad,
> > > > >>>
> > > > >>>
> > > > >> All of ytex has been moved into ctakes, it is currently in a
> > > > >> branch (
> > > > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You
> > > > >>> don't have to install ytex-0.8 - instead you will have to
> > > > >>> build and install from the ytex branch to create your own
> > > > >>> distribution. Steps
> > > 2 & 3
> > > > are correct.
> > > > >>>
> > > > >>> Although it is a pain, if you have the jdk, maven, and svn,
> > > > >>> you can easily build your own distro:
> > > > >>> * open a command prompt
> > > > >>> * make sure jdk, maven, and svn are in your path
> > > > >>> * cd to some directory where you want to check stuff out (I
> > > > >>> like
> > > > >>> c:\temp)
> > > > >>> * run the following commands
> > > > >>> rmdir /s /q ctakes
> > > > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex
> > > > >>> ctakes cd ctakes mvn clean install -DskipTests
> > > > >>>
> > > > >>> And you will have the ctakes (with ytex) distro in
> > > > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT
> > > > >>> -b
> > > > >>> in.z
> > > > >>> ip
> > > > >>>
> > > > >>> What is the process for getting the ytex branch merged into
> trunk?
> > > > >>> As I mentioned, there are very few changes to other ctakes
> > > > >>> classes/types - this should be completely complementary and
> > > > >>> not affect any existing ctakes functionality.
> > > > >>>
> > > > >>> -vj
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> > > > >>>
> > > > >>>> Hi VJ--
> > > > >>>>
> > > > >>>> this is great!! Thanks for all the hard work on it!
> > > > >>>>
> > > > >>>> We're starting to look into the new install. For now we're
> > > > >>>> trying the binaries out.
> > > > >>>>
> > > > >>>> There were these questions about the proper install steps:
> > > > >>>>
> > > > >>>> 1. Do we first install ytex-0.8 2. Then install the new
> > > > >>>> cTakes
> > > > >>>> 3.1.1 instance and also apply the SNAPSHOT lib and resources
> > > > >>>> zips 3. Work our way to install the UMLS ontologies in the db
> > > > >>>>
> > > > >>>> Its is not entirely clear from the new document (
> > > > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> > > > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> > > > >>>> if there's still need to install ytex-0.8, or YTEX has been
> > > > >>>> entirely merged into cTakes?
> > > > >>>>
> > > > >>>> If the last statement is correct, there are missing parts in
> > > > >>>> i.e the UMLS install steps that are linked from the new
> > > > >>>> ctakes
> > > > >>>> 3.1.1
> > > > document.
> > > > >>>>
> > > > >>>> Thanks,
> > > > >>>> vlad
> > > > >>>>
> > > > >>>>
> > > > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> > > > >>>>>
> > > > >>>>> Hello All,
> > > > >>>>>
> > > > >>>>> I have finished an initial cut at the port of YTEX to cTAKES
> > 3.1.1.
> > > > >>>>> Most of the YTEX functionality has been ported and
> > > > >>>>> integrated with cTAKES, and I've tested with MySQL and MS
> > > > >>>>> SQL Server (oracle
> > > > tests pending).
> > > > >>>>>
> > > > >>>>> Most of the changes were made in new projects - very little
> > > > >>>>> existing cTAKES code has been modified. The only
> > > > >>>>> non-trivial changes are in
> > > > >>>>> /ctakes-
> > > > assertion/src/main/java/org/apache/ctakes/assertion/medfac
> > > > >>>>> ts/i2b2/api
> > > > >>>>> - here I modified
> > > > >>>>> CharacterOffsetToLineTokenConverterCtakesImpl &
> > > > >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> > > > >>>>> sentences correctly. Can somebody take a look at the
> > > > >>>>> changes in
> > > the
> > > > ytex branch?
> > > > >>>>>
> > > > >>>>> I believe that the branch https://svn.apache.org/
> > > > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into
> > > > >>>>> ctakes trunk, but would like other users to test it as well.
> > Questions:
> > > > >>>>>
> > > > >>>>> * How can I distribute the ctakes binary distribution to
> > > > >>>>> ytex users before the merge? Can we make the branch build
> > > > >>>>> available somewhere? The binary distribution is too large
> > > > >>>>> to host on the ytex google code site (max
> > > > >>>>> 200 MB)
> > > > >>>>> * Non-ASF libraries - I have segregated these out into their
> > > > >>>>> own zip file that can be distributed via sourceforge. As a
> > > > >>>>> stopgap, I can upload this to the ytex google code site, but
> > > > >>>>> would prefer to upload to sourceforge.
> > > > >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> > > > >>>>> sourceforge.
> > > > >>>>> * Documentation - How can I update the confluence docs? I
> > > > >>>>> would migrate the documentation from the google code website.
> > > > >>>>>
> > > > >>>>> Here the installation instructions (putting the wagon in
> > > > >>>>> front of the horse ...)
> > > > >>>>>
> > > > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> > > > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> > > > >>>>>
> > > > >>>>> Best,
> > > > >>>>>
> > > > >>>>> VJ
> > > > >>>>>
> > > > >>>>>
> > > > >>>>> --
> > > > >>>> You received this message because you are subscribed to the
> > > > >>>> Google Groups "ytex-users" group.
> > > > >>>> To unsubscribe from this group and stop receiving emails from
> > > > >>>> it, send an email to ytex-users+...@googlegroups.com.
> > > > >>>> To post to this group, send email to ytex-...@googlegroups.com.
> > > > >>>> To view this discussion on the web visit
> > > > >>>> https://groups.google.com/d/
> > > > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> > > > >>>> 40googlegroups.com.
> > > > >>>>
> > > > >>>> For more options, visit
> https://groups.google.com/groups/opt_out.
> > > > >>>>
> > > > >>>
> > > > >>> --
> > > > >> You received this message because you are subscribed to the
> > > > >> Google Groups "ytex-users" group.
> > > > >> To unsubscribe from this group and stop receiving emails from
> > > > >> it, send an email to ytex-users+unsubscribe@googlegroups.com.
> > > > >> To post to this group, send email to ytex-users@googlegroups.com.
> > > > >> To view this discussion on the web visit
> > > > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd
> > > > >> -
> > > > a273-
> > > > >> a3b1a7b36241%40googlegroups.com .
> > > > >>
> > > > >> For more options, visit https://groups.google.com/groups/opt_out.
> > > > >>
> > > > >
> > > > >
> > >
> >
>
RE: YTEX cTAKES 3.1.1 ready
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Right, got it. I just wanted to let you know that some EMR notes -do- require sentence splitting at newline characters.
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Thursday, February 06, 2014 1:06 PM
To: dev@ctakes.apache.org
Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org; vlad.valtchinov@gmail.com
Subject: Re: YTEX cTAKES 3.1.1 ready
The cTAKES sentence detector is not changed in the YTEX branch. The YTEX branch has an *additional* sentence detector that does not automatically split sentences on newlines - users can use this if they like.
-vj
On Thu, Feb 6, 2014 at 1:01 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Hi Vijay,
>
> > I have yet to run across clinical text from a real EMR where
> > newlines
> represent the end of a sentence
>
> Since James pointed out this possibility a couple weeks ago, I have
> kept my eyes open. The problem is pretty ubiquitous in a corpus that
> I'm working with right now. I just opened the first note and gave it
> a count ... 95 lines total, 9 are sentence/phrase (lacking punctuation) endings.
> This is not including lists, which comprise about half of the note.
> One possible conjoinment was "Will consider [...] biopsy\nGiven [...]".
> Depending upon how cTakes deals with it, the meaning could change
> drastically.
>
> > I believe cTAKES absolutely has to support sentences with newlines
> within them
>
> Yes, cTakes should do so, but I hope that you aren't suggesting that
> it only support such a structure.
>
> Where is that easy button?
>
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Thursday, February 06, 2014 10:31 AM
> To: dev@ctakes.apache.org
> Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> vlad.valtchinov@gmail.com
> Subject: Re: YTEX cTAKES 3.1.1 ready
>
> I believe it is worth migrating to trunk.
>
> Note that the sentence detector is also complementary - the existing
> ctakes sentence detector is unchanged - users can choose which
> sentence detector to use. There are changes to assertion & dependency
> parsing to support sentences without newlines, and that works with
> both sentence detectors.
>
> I believe cTAKES absolutely has to support sentences with newlines
> within them - I have yet to run across clinical text from a real EMR
> where newlines represent the end of a sentence - the changes to
> assertion & dependency parsing will have to be done at some point.
>
> -vj
>
>
> On Thu, Feb 6, 2014 at 10:19 AM, Chen, Pei
> <Pe...@childrens.harvard.edu>wrote:
>
> > VJ,
> > Aside from the changes to the existing cTAKES code (sentence
> > detector,
> > etc.) [which we could leave out if it's still being debated], Do you
> > think it's worth migrating the ytex code to trunk at this point?
> > As you mentioned earlier, it's largely complementary.
> > [I was just thinking of saving effort to maintain the separate
> > branch and for simplicity for dev...]
> >
> > --Pei
> >
> > > -----Original Message-----
> > > From: vijay garla [mailto:vngarla@gmail.com]
> > > Sent: Wednesday, February 05, 2014 9:30 PM
> > > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > > vlad.valtchinov@gmail.com
> > > Subject: Re: YTEX cTAKES 3.1.1 ready
> > >
> > > Hi Vlad,
> > >
> > > I Updated the umls install guide; see
> > > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> > >
> > > I would prefer to add the docs in the ctakes confluence, but as
> > > far as I
> > can
> > > tell, I don't have write access there - can somebody give me write
> > privileges
> > > on the ctakes confluence site?
> > >
> > > There was a bug in the umls install; copy
> > > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> > > ytex/scripts/data/build.xmlover
> > > the corresponding file in your ctakes-3.1.2 install
> > > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set.
> > > The import is currently running on the UMLS 2013AA (I assume this
> > > will
> > complete
> > > without issues as long as the umls schema hasn't changed from 2012).
> > >
> > > what trial and error did you have to go through to build the distro?
> > >
> > > -vj
> > >
> > >
> > > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> > >
> > > > Hi Vlad,
> > > >
> > > > sorry that the instructions aren't clear.
> > > >
> > > > re 1) What I am trying to say is install
> > > > apache-ctakes-3.2.0-snapshot as usual (this is unchanged from
> > > > 3.1.1). After that you still have to apply the lib and
> > > > resources (these are things that cannot be distributed via apache).
> > > >
> > > > re 2) Yes, I need to update those docs. Hopefully will get to
> > > > that at some point. However, I assume you already have a UMLS
> > > > DB (also assume SQL Server). If you can't/don't want to use
> > > > your existing umls DB, please tell me. The I'll priortize
> > > > upgrading the doc on importing the umls tables (the scripts are there).
> > > >
> > > > best,
> > > >
> > > > VJ
> > > >
> > > >
> > > > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> > > >
> > > >> Hi VJ-
> > > >>
> > > >> so, with trial and error were able to make the distribution and
> > > >> now have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> > > >>
> > > >> Here's what's unclear.
> > > >>
> > > >> 1. Is now this the only (combined) thing that you need for
> > > >> ctakes
> > > >> 3.1.1 + Ytex?
> > > >> the current documentation (https://code.google.com/p/yte
> > > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> > > >> lation_cTAKES_3_1)
> > > >> which most probably is outdated, talks about installing cTakes
> > > >> 3.1.1 first and then applying 2 SNAPSHOT archives
> > > >> (downloadable) , lib and resources.
> > > >> This is a confusion point.
> > > >>
> > > >> 2. The directions to import UMLS subset are then outdated as well.
> > > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8)
> > > >> to import the RRF files for the UMLS subset and then just use
> > > >> the resulting db. Thoughts?
> > > >>
> > > >> Thanks,
> > > >> Vlad Valtchinov
> > > >> Brigham Rad
> > > >>
> > > >>
> > > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> > > >>
> > > >>> Hi Vlad,
> > > >>>
> > > >>>
> > > >> All of ytex has been moved into ctakes, it is currently in a
> > > >> branch (
> > > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You
> > > >>> don't have to install ytex-0.8 - instead you will have to
> > > >>> build and install from the ytex branch to create your own
> > > >>> distribution. Steps
> > 2 & 3
> > > are correct.
> > > >>>
> > > >>> Although it is a pain, if you have the jdk, maven, and svn,
> > > >>> you can easily build your own distro:
> > > >>> * open a command prompt
> > > >>> * make sure jdk, maven, and svn are in your path
> > > >>> * cd to some directory where you want to check stuff out (I
> > > >>> like
> > > >>> c:\temp)
> > > >>> * run the following commands
> > > >>> rmdir /s /q ctakes
> > > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex
> > > >>> ctakes cd ctakes mvn clean install -DskipTests
> > > >>>
> > > >>> And you will have the ctakes (with ytex) distro in
> > > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT
> > > >>> -b
> > > >>> in.z
> > > >>> ip
> > > >>>
> > > >>> What is the process for getting the ytex branch merged into trunk?
> > > >>> As I mentioned, there are very few changes to other ctakes
> > > >>> classes/types - this should be completely complementary and
> > > >>> not affect any existing ctakes functionality.
> > > >>>
> > > >>> -vj
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> > > >>>
> > > >>>> Hi VJ--
> > > >>>>
> > > >>>> this is great!! Thanks for all the hard work on it!
> > > >>>>
> > > >>>> We're starting to look into the new install. For now we're
> > > >>>> trying the binaries out.
> > > >>>>
> > > >>>> There were these questions about the proper install steps:
> > > >>>>
> > > >>>> 1. Do we first install ytex-0.8 2. Then install the new
> > > >>>> cTakes
> > > >>>> 3.1.1 instance and also apply the SNAPSHOT lib and resources
> > > >>>> zips 3. Work our way to install the UMLS ontologies in the db
> > > >>>>
> > > >>>> Its is not entirely clear from the new document (
> > > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> > > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> > > >>>> if there's still need to install ytex-0.8, or YTEX has been
> > > >>>> entirely merged into cTakes?
> > > >>>>
> > > >>>> If the last statement is correct, there are missing parts in
> > > >>>> i.e the UMLS install steps that are linked from the new
> > > >>>> ctakes
> > > >>>> 3.1.1
> > > document.
> > > >>>>
> > > >>>> Thanks,
> > > >>>> vlad
> > > >>>>
> > > >>>>
> > > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> > > >>>>>
> > > >>>>> Hello All,
> > > >>>>>
> > > >>>>> I have finished an initial cut at the port of YTEX to cTAKES
> 3.1.1.
> > > >>>>> Most of the YTEX functionality has been ported and
> > > >>>>> integrated with cTAKES, and I've tested with MySQL and MS
> > > >>>>> SQL Server (oracle
> > > tests pending).
> > > >>>>>
> > > >>>>> Most of the changes were made in new projects - very little
> > > >>>>> existing cTAKES code has been modified. The only
> > > >>>>> non-trivial changes are in
> > > >>>>> /ctakes-
> > > assertion/src/main/java/org/apache/ctakes/assertion/medfac
> > > >>>>> ts/i2b2/api
> > > >>>>> - here I modified
> > > >>>>> CharacterOffsetToLineTokenConverterCtakesImpl &
> > > >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> > > >>>>> sentences correctly. Can somebody take a look at the
> > > >>>>> changes in
> > the
> > > ytex branch?
> > > >>>>>
> > > >>>>> I believe that the branch https://svn.apache.org/
> > > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into
> > > >>>>> ctakes trunk, but would like other users to test it as well.
> Questions:
> > > >>>>>
> > > >>>>> * How can I distribute the ctakes binary distribution to
> > > >>>>> ytex users before the merge? Can we make the branch build
> > > >>>>> available somewhere? The binary distribution is too large
> > > >>>>> to host on the ytex google code site (max
> > > >>>>> 200 MB)
> > > >>>>> * Non-ASF libraries - I have segregated these out into their
> > > >>>>> own zip file that can be distributed via sourceforge. As a
> > > >>>>> stopgap, I can upload this to the ytex google code site, but
> > > >>>>> would prefer to upload to sourceforge.
> > > >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> > > >>>>> sourceforge.
> > > >>>>> * Documentation - How can I update the confluence docs? I
> > > >>>>> would migrate the documentation from the google code website.
> > > >>>>>
> > > >>>>> Here the installation instructions (putting the wagon in
> > > >>>>> front of the horse ...)
> > > >>>>>
> > > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> > > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> > > >>>>>
> > > >>>>> Best,
> > > >>>>>
> > > >>>>> VJ
> > > >>>>>
> > > >>>>>
> > > >>>>> --
> > > >>>> You received this message because you are subscribed to the
> > > >>>> Google Groups "ytex-users" group.
> > > >>>> To unsubscribe from this group and stop receiving emails from
> > > >>>> it, send an email to ytex-users+...@googlegroups.com.
> > > >>>> To post to this group, send email to ytex-...@googlegroups.com.
> > > >>>> To view this discussion on the web visit
> > > >>>> https://groups.google.com/d/
> > > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> > > >>>> 40googlegroups.com.
> > > >>>>
> > > >>>> For more options, visit https://groups.google.com/groups/opt_out.
> > > >>>>
> > > >>>
> > > >>> --
> > > >> You received this message because you are subscribed to the
> > > >> Google Groups "ytex-users" group.
> > > >> To unsubscribe from this group and stop receiving emails from
> > > >> it, send an email to ytex-users+unsubscribe@googlegroups.com.
> > > >> To post to this group, send email to ytex-users@googlegroups.com.
> > > >> To view this discussion on the web visit
> > > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd
> > > >> -
> > > a273-
> > > >> a3b1a7b36241%40googlegroups.com .
> > > >>
> > > >> For more options, visit https://groups.google.com/groups/opt_out.
> > > >>
> > > >
> > > >
> >
>
Re: YTEX cTAKES 3.1.1 ready
Posted by vijay garla <vn...@gmail.com>.
The cTAKES sentence detector is not changed in the YTEX branch. The YTEX
branch has an *additional* sentence detector that does not automatically
split sentences on newlines - users can use this if they like.
-vj
On Thu, Feb 6, 2014 at 1:01 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Vijay,
>
> > I have yet to run across clinical text from a real EMR where newlines
> represent the end of a sentence
>
> Since James pointed out this possibility a couple weeks ago, I have kept
> my eyes open. The problem is pretty ubiquitous in a corpus that I'm
> working with right now. I just opened the first note and gave it a count
> ... 95 lines total, 9 are sentence/phrase (lacking punctuation) endings.
> This is not including lists, which comprise about half of the note.
> One possible conjoinment was "Will consider [...] biopsy\nGiven [...]".
> Depending upon how cTakes deals with it, the meaning could change
> drastically.
>
> > I believe cTAKES absolutely has to support sentences with newlines
> within them
>
> Yes, cTakes should do so, but I hope that you aren't suggesting that it
> only support such a structure.
>
> Where is that easy button?
>
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Thursday, February 06, 2014 10:31 AM
> To: dev@ctakes.apache.org
> Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> vlad.valtchinov@gmail.com
> Subject: Re: YTEX cTAKES 3.1.1 ready
>
> I believe it is worth migrating to trunk.
>
> Note that the sentence detector is also complementary - the existing
> ctakes sentence detector is unchanged - users can choose which sentence
> detector to use. There are changes to assertion & dependency parsing to
> support sentences without newlines, and that works with both sentence
> detectors.
>
> I believe cTAKES absolutely has to support sentences with newlines within
> them - I have yet to run across clinical text from a real EMR where
> newlines represent the end of a sentence - the changes to assertion &
> dependency parsing will have to be done at some point.
>
> -vj
>
>
> On Thu, Feb 6, 2014 at 10:19 AM, Chen, Pei
> <Pe...@childrens.harvard.edu>wrote:
>
> > VJ,
> > Aside from the changes to the existing cTAKES code (sentence detector,
> > etc.) [which we could leave out if it's still being debated], Do you
> > think it's worth migrating the ytex code to trunk at this point?
> > As you mentioned earlier, it's largely complementary.
> > [I was just thinking of saving effort to maintain the separate branch
> > and for simplicity for dev...]
> >
> > --Pei
> >
> > > -----Original Message-----
> > > From: vijay garla [mailto:vngarla@gmail.com]
> > > Sent: Wednesday, February 05, 2014 9:30 PM
> > > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > > vlad.valtchinov@gmail.com
> > > Subject: Re: YTEX cTAKES 3.1.1 ready
> > >
> > > Hi Vlad,
> > >
> > > I Updated the umls install guide; see
> > > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> > >
> > > I would prefer to add the docs in the ctakes confluence, but as far
> > > as I
> > can
> > > tell, I don't have write access there - can somebody give me write
> > privileges
> > > on the ctakes confluence site?
> > >
> > > There was a bug in the umls install; copy
> > > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> > > ytex/scripts/data/build.xmlover
> > > the corresponding file in your ctakes-3.1.2 install
> > > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set.
> > > The import is currently running on the UMLS 2013AA (I assume this
> > > will
> > complete
> > > without issues as long as the umls schema hasn't changed from 2012).
> > >
> > > what trial and error did you have to go through to build the distro?
> > >
> > > -vj
> > >
> > >
> > > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> > >
> > > > Hi Vlad,
> > > >
> > > > sorry that the instructions aren't clear.
> > > >
> > > > re 1) What I am trying to say is install
> > > > apache-ctakes-3.2.0-snapshot as usual (this is unchanged from
> > > > 3.1.1). After that you still have to apply the lib and resources
> > > > (these are things that cannot be distributed via apache).
> > > >
> > > > re 2) Yes, I need to update those docs. Hopefully will get to
> > > > that at some point. However, I assume you already have a UMLS DB
> > > > (also assume SQL Server). If you can't/don't want to use your
> > > > existing umls DB, please tell me. The I'll priortize upgrading
> > > > the doc on importing the umls tables (the scripts are there).
> > > >
> > > > best,
> > > >
> > > > VJ
> > > >
> > > >
> > > > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> > > >
> > > >> Hi VJ-
> > > >>
> > > >> so, with trial and error were able to make the distribution and
> > > >> now have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> > > >>
> > > >> Here's what's unclear.
> > > >>
> > > >> 1. Is now this the only (combined) thing that you need for ctakes
> > > >> 3.1.1 + Ytex?
> > > >> the current documentation (https://code.google.com/p/yte
> > > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> > > >> lation_cTAKES_3_1)
> > > >> which most probably is outdated, talks about installing cTakes
> > > >> 3.1.1 first and then applying 2 SNAPSHOT archives (downloadable)
> > > >> , lib and resources.
> > > >> This is a confusion point.
> > > >>
> > > >> 2. The directions to import UMLS subset are then outdated as well.
> > > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to
> > > >> import the RRF files for the UMLS subset and then just use the
> > > >> resulting db. Thoughts?
> > > >>
> > > >> Thanks,
> > > >> Vlad Valtchinov
> > > >> Brigham Rad
> > > >>
> > > >>
> > > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> > > >>
> > > >>> Hi Vlad,
> > > >>>
> > > >>>
> > > >> All of ytex has been moved into ctakes, it is currently in a
> > > >> branch (
> > > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You
> > > >>> don't have to install ytex-0.8 - instead you will have to build
> > > >>> and install from the ytex branch to create your own
> > > >>> distribution. Steps
> > 2 & 3
> > > are correct.
> > > >>>
> > > >>> Although it is a pain, if you have the jdk, maven, and svn, you
> > > >>> can easily build your own distro:
> > > >>> * open a command prompt
> > > >>> * make sure jdk, maven, and svn are in your path
> > > >>> * cd to some directory where you want to check stuff out (I like
> > > >>> c:\temp)
> > > >>> * run the following commands
> > > >>> rmdir /s /q ctakes
> > > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex
> > > >>> ctakes cd ctakes mvn clean install -DskipTests
> > > >>>
> > > >>> And you will have the ctakes (with ytex) distro in
> > > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-b
> > > >>> in.z
> > > >>> ip
> > > >>>
> > > >>> What is the process for getting the ytex branch merged into trunk?
> > > >>> As I mentioned, there are very few changes to other ctakes
> > > >>> classes/types - this should be completely complementary and not
> > > >>> affect any existing ctakes functionality.
> > > >>>
> > > >>> -vj
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> > > >>>
> > > >>>> Hi VJ--
> > > >>>>
> > > >>>> this is great!! Thanks for all the hard work on it!
> > > >>>>
> > > >>>> We're starting to look into the new install. For now we're
> > > >>>> trying the binaries out.
> > > >>>>
> > > >>>> There were these questions about the proper install steps:
> > > >>>>
> > > >>>> 1. Do we first install ytex-0.8 2. Then install the new cTakes
> > > >>>> 3.1.1 instance and also apply the SNAPSHOT lib and resources
> > > >>>> zips 3. Work our way to install the UMLS ontologies in the db
> > > >>>>
> > > >>>> Its is not entirely clear from the new document (
> > > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> > > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> > > >>>> if there's still need to install ytex-0.8, or YTEX has been
> > > >>>> entirely merged into cTakes?
> > > >>>>
> > > >>>> If the last statement is correct, there are missing parts in
> > > >>>> i.e the UMLS install steps that are linked from the new ctakes
> > > >>>> 3.1.1
> > > document.
> > > >>>>
> > > >>>> Thanks,
> > > >>>> vlad
> > > >>>>
> > > >>>>
> > > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> > > >>>>>
> > > >>>>> Hello All,
> > > >>>>>
> > > >>>>> I have finished an initial cut at the port of YTEX to cTAKES
> 3.1.1.
> > > >>>>> Most of the YTEX functionality has been ported and integrated
> > > >>>>> with cTAKES, and I've tested with MySQL and MS SQL Server
> > > >>>>> (oracle
> > > tests pending).
> > > >>>>>
> > > >>>>> Most of the changes were made in new projects - very little
> > > >>>>> existing cTAKES code has been modified. The only non-trivial
> > > >>>>> changes are in
> > > >>>>> /ctakes-
> > > assertion/src/main/java/org/apache/ctakes/assertion/medfac
> > > >>>>> ts/i2b2/api
> > > >>>>> - here I modified
> > > >>>>> CharacterOffsetToLineTokenConverterCtakesImpl &
> > > >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> > > >>>>> sentences correctly. Can somebody take a look at the changes
> > > >>>>> in
> > the
> > > ytex branch?
> > > >>>>>
> > > >>>>> I believe that the branch https://svn.apache.org/
> > > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into
> > > >>>>> ctakes trunk, but would like other users to test it as well.
> Questions:
> > > >>>>>
> > > >>>>> * How can I distribute the ctakes binary distribution to ytex
> > > >>>>> users before the merge? Can we make the branch build available
> > > >>>>> somewhere? The binary distribution is too large to host on
> > > >>>>> the ytex google code site (max
> > > >>>>> 200 MB)
> > > >>>>> * Non-ASF libraries - I have segregated these out into their
> > > >>>>> own zip file that can be distributed via sourceforge. As a
> > > >>>>> stopgap, I can upload this to the ytex google code site, but
> > > >>>>> would prefer to upload to sourceforge.
> > > >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> > > >>>>> sourceforge.
> > > >>>>> * Documentation - How can I update the confluence docs? I
> > > >>>>> would migrate the documentation from the google code website.
> > > >>>>>
> > > >>>>> Here the installation instructions (putting the wagon in front
> > > >>>>> of the horse ...)
> > > >>>>>
> > > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> > > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> > > >>>>>
> > > >>>>> Best,
> > > >>>>>
> > > >>>>> VJ
> > > >>>>>
> > > >>>>>
> > > >>>>> --
> > > >>>> You received this message because you are subscribed to the
> > > >>>> Google Groups "ytex-users" group.
> > > >>>> To unsubscribe from this group and stop receiving emails from
> > > >>>> it, send an email to ytex-users+...@googlegroups.com.
> > > >>>> To post to this group, send email to ytex-...@googlegroups.com.
> > > >>>> To view this discussion on the web visit
> > > >>>> https://groups.google.com/d/
> > > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> > > >>>> 40googlegroups.com.
> > > >>>>
> > > >>>> For more options, visit https://groups.google.com/groups/opt_out.
> > > >>>>
> > > >>>
> > > >>> --
> > > >> You received this message because you are subscribed to the
> > > >> Google Groups "ytex-users" group.
> > > >> To unsubscribe from this group and stop receiving emails from it,
> > > >> send an email to ytex-users+unsubscribe@googlegroups.com.
> > > >> To post to this group, send email to ytex-users@googlegroups.com.
> > > >> To view this discussion on the web visit
> > > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-
> > > a273-
> > > >> a3b1a7b36241%40googlegroups.com
> > > >> .
> > > >>
> > > >> For more options, visit https://groups.google.com/groups/opt_out.
> > > >>
> > > >
> > > >
> >
>
RE: YTEX cTAKES 3.1.1 ready
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Vijay,
> I have yet to run across clinical text from a real EMR where newlines represent the end of a sentence
Since James pointed out this possibility a couple weeks ago, I have kept my eyes open. The problem is pretty ubiquitous in a corpus that I'm working with right now. I just opened the first note and gave it a count ... 95 lines total, 9 are sentence/phrase (lacking punctuation) endings. This is not including lists, which comprise about half of the note.
One possible conjoinment was "Will consider [...] biopsy\nGiven [...]". Depending upon how cTakes deals with it, the meaning could change drastically.
> I believe cTAKES absolutely has to support sentences with newlines within them
Yes, cTakes should do so, but I hope that you aren't suggesting that it only support such a structure.
Where is that easy button?
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Thursday, February 06, 2014 10:31 AM
To: dev@ctakes.apache.org
Cc: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org; vlad.valtchinov@gmail.com
Subject: Re: YTEX cTAKES 3.1.1 ready
I believe it is worth migrating to trunk.
Note that the sentence detector is also complementary - the existing ctakes sentence detector is unchanged - users can choose which sentence detector to use. There are changes to assertion & dependency parsing to support sentences without newlines, and that works with both sentence detectors.
I believe cTAKES absolutely has to support sentences with newlines within them - I have yet to run across clinical text from a real EMR where newlines represent the end of a sentence - the changes to assertion & dependency parsing will have to be done at some point.
-vj
On Thu, Feb 6, 2014 at 10:19 AM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> VJ,
> Aside from the changes to the existing cTAKES code (sentence detector,
> etc.) [which we could leave out if it's still being debated], Do you
> think it's worth migrating the ytex code to trunk at this point?
> As you mentioned earlier, it's largely complementary.
> [I was just thinking of saving effort to maintain the separate branch
> and for simplicity for dev...]
>
> --Pei
>
> > -----Original Message-----
> > From: vijay garla [mailto:vngarla@gmail.com]
> > Sent: Wednesday, February 05, 2014 9:30 PM
> > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > vlad.valtchinov@gmail.com
> > Subject: Re: YTEX cTAKES 3.1.1 ready
> >
> > Hi Vlad,
> >
> > I Updated the umls install guide; see
> > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> >
> > I would prefer to add the docs in the ctakes confluence, but as far
> > as I
> can
> > tell, I don't have write access there - can somebody give me write
> privileges
> > on the ctakes confluence site?
> >
> > There was a bug in the umls install; copy
> > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> > ytex/scripts/data/build.xmlover
> > the corresponding file in your ctakes-3.1.2 install
> > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set.
> > The import is currently running on the UMLS 2013AA (I assume this
> > will
> complete
> > without issues as long as the umls schema hasn't changed from 2012).
> >
> > what trial and error did you have to go through to build the distro?
> >
> > -vj
> >
> >
> > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> >
> > > Hi Vlad,
> > >
> > > sorry that the instructions aren't clear.
> > >
> > > re 1) What I am trying to say is install
> > > apache-ctakes-3.2.0-snapshot as usual (this is unchanged from
> > > 3.1.1). After that you still have to apply the lib and resources
> > > (these are things that cannot be distributed via apache).
> > >
> > > re 2) Yes, I need to update those docs. Hopefully will get to
> > > that at some point. However, I assume you already have a UMLS DB
> > > (also assume SQL Server). If you can't/don't want to use your
> > > existing umls DB, please tell me. The I'll priortize upgrading
> > > the doc on importing the umls tables (the scripts are there).
> > >
> > > best,
> > >
> > > VJ
> > >
> > >
> > > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> > >
> > >> Hi VJ-
> > >>
> > >> so, with trial and error were able to make the distribution and
> > >> now have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> > >>
> > >> Here's what's unclear.
> > >>
> > >> 1. Is now this the only (combined) thing that you need for ctakes
> > >> 3.1.1 + Ytex?
> > >> the current documentation (https://code.google.com/p/yte
> > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> > >> lation_cTAKES_3_1)
> > >> which most probably is outdated, talks about installing cTakes
> > >> 3.1.1 first and then applying 2 SNAPSHOT archives (downloadable)
> > >> , lib and resources.
> > >> This is a confusion point.
> > >>
> > >> 2. The directions to import UMLS subset are then outdated as well.
> > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to
> > >> import the RRF files for the UMLS subset and then just use the
> > >> resulting db. Thoughts?
> > >>
> > >> Thanks,
> > >> Vlad Valtchinov
> > >> Brigham Rad
> > >>
> > >>
> > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> > >>
> > >>> Hi Vlad,
> > >>>
> > >>>
> > >> All of ytex has been moved into ctakes, it is currently in a
> > >> branch (
> > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You
> > >>> don't have to install ytex-0.8 - instead you will have to build
> > >>> and install from the ytex branch to create your own
> > >>> distribution. Steps
> 2 & 3
> > are correct.
> > >>>
> > >>> Although it is a pain, if you have the jdk, maven, and svn, you
> > >>> can easily build your own distro:
> > >>> * open a command prompt
> > >>> * make sure jdk, maven, and svn are in your path
> > >>> * cd to some directory where you want to check stuff out (I like
> > >>> c:\temp)
> > >>> * run the following commands
> > >>> rmdir /s /q ctakes
> > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex
> > >>> ctakes cd ctakes mvn clean install -DskipTests
> > >>>
> > >>> And you will have the ctakes (with ytex) distro in
> > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-b
> > >>> in.z
> > >>> ip
> > >>>
> > >>> What is the process for getting the ytex branch merged into trunk?
> > >>> As I mentioned, there are very few changes to other ctakes
> > >>> classes/types - this should be completely complementary and not
> > >>> affect any existing ctakes functionality.
> > >>>
> > >>> -vj
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> > >>>
> > >>>> Hi VJ--
> > >>>>
> > >>>> this is great!! Thanks for all the hard work on it!
> > >>>>
> > >>>> We're starting to look into the new install. For now we're
> > >>>> trying the binaries out.
> > >>>>
> > >>>> There were these questions about the proper install steps:
> > >>>>
> > >>>> 1. Do we first install ytex-0.8 2. Then install the new cTakes
> > >>>> 3.1.1 instance and also apply the SNAPSHOT lib and resources
> > >>>> zips 3. Work our way to install the UMLS ontologies in the db
> > >>>>
> > >>>> Its is not entirely clear from the new document (
> > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> > >>>> if there's still need to install ytex-0.8, or YTEX has been
> > >>>> entirely merged into cTakes?
> > >>>>
> > >>>> If the last statement is correct, there are missing parts in
> > >>>> i.e the UMLS install steps that are linked from the new ctakes
> > >>>> 3.1.1
> > document.
> > >>>>
> > >>>> Thanks,
> > >>>> vlad
> > >>>>
> > >>>>
> > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> > >>>>>
> > >>>>> Hello All,
> > >>>>>
> > >>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
> > >>>>> Most of the YTEX functionality has been ported and integrated
> > >>>>> with cTAKES, and I've tested with MySQL and MS SQL Server
> > >>>>> (oracle
> > tests pending).
> > >>>>>
> > >>>>> Most of the changes were made in new projects - very little
> > >>>>> existing cTAKES code has been modified. The only non-trivial
> > >>>>> changes are in
> > >>>>> /ctakes-
> > assertion/src/main/java/org/apache/ctakes/assertion/medfac
> > >>>>> ts/i2b2/api
> > >>>>> - here I modified
> > >>>>> CharacterOffsetToLineTokenConverterCtakesImpl &
> > >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> > >>>>> sentences correctly. Can somebody take a look at the changes
> > >>>>> in
> the
> > ytex branch?
> > >>>>>
> > >>>>> I believe that the branch https://svn.apache.org/
> > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into
> > >>>>> ctakes trunk, but would like other users to test it as well. Questions:
> > >>>>>
> > >>>>> * How can I distribute the ctakes binary distribution to ytex
> > >>>>> users before the merge? Can we make the branch build available
> > >>>>> somewhere? The binary distribution is too large to host on
> > >>>>> the ytex google code site (max
> > >>>>> 200 MB)
> > >>>>> * Non-ASF libraries - I have segregated these out into their
> > >>>>> own zip file that can be distributed via sourceforge. As a
> > >>>>> stopgap, I can upload this to the ytex google code site, but
> > >>>>> would prefer to upload to sourceforge.
> > >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> > >>>>> sourceforge.
> > >>>>> * Documentation - How can I update the confluence docs? I
> > >>>>> would migrate the documentation from the google code website.
> > >>>>>
> > >>>>> Here the installation instructions (putting the wagon in front
> > >>>>> of the horse ...)
> > >>>>>
> > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> > >>>>>
> > >>>>> Best,
> > >>>>>
> > >>>>> VJ
> > >>>>>
> > >>>>>
> > >>>>> --
> > >>>> You received this message because you are subscribed to the
> > >>>> Google Groups "ytex-users" group.
> > >>>> To unsubscribe from this group and stop receiving emails from
> > >>>> it, send an email to ytex-users+...@googlegroups.com.
> > >>>> To post to this group, send email to ytex-...@googlegroups.com.
> > >>>> To view this discussion on the web visit
> > >>>> https://groups.google.com/d/
> > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> > >>>> 40googlegroups.com.
> > >>>>
> > >>>> For more options, visit https://groups.google.com/groups/opt_out.
> > >>>>
> > >>>
> > >>> --
> > >> You received this message because you are subscribed to the
> > >> Google Groups "ytex-users" group.
> > >> To unsubscribe from this group and stop receiving emails from it,
> > >> send an email to ytex-users+unsubscribe@googlegroups.com.
> > >> To post to this group, send email to ytex-users@googlegroups.com.
> > >> To view this discussion on the web visit
> > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-
> > a273-
> > >> a3b1a7b36241%40googlegroups.com
> > >> .
> > >>
> > >> For more options, visit https://groups.google.com/groups/opt_out.
> > >>
> > >
> > >
>
Re: YTEX cTAKES 3.1.1 ready
Posted by vijay garla <vn...@gmail.com>.
I believe it is worth migrating to trunk.
Note that the sentence detector is also complementary - the existing ctakes
sentence detector is unchanged - users can choose which sentence detector
to use. There are changes to assertion & dependency parsing to support
sentences without newlines, and that works with both sentence detectors.
I believe cTAKES absolutely has to support sentences with newlines within
them - I have yet to run across clinical text from a real EMR where
newlines represent the end of a sentence - the changes to assertion &
dependency parsing will have to be done at some point.
-vj
On Thu, Feb 6, 2014 at 10:19 AM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> VJ,
> Aside from the changes to the existing cTAKES code (sentence detector,
> etc.) [which we could leave out if it's still being debated],
> Do you think it's worth migrating the ytex code to trunk at this point?
> As you mentioned earlier, it's largely complementary.
> [I was just thinking of saving effort to maintain the separate branch and
> for simplicity for dev...]
>
> --Pei
>
> > -----Original Message-----
> > From: vijay garla [mailto:vngarla@gmail.com]
> > Sent: Wednesday, February 05, 2014 9:30 PM
> > To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> > vlad.valtchinov@gmail.com
> > Subject: Re: YTEX cTAKES 3.1.1 ready
> >
> > Hi Vlad,
> >
> > I Updated the umls install guide; see
> > https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
> >
> > I would prefer to add the docs in the ctakes confluence, but as far as I
> can
> > tell, I don't have write access there - can somebody give me write
> privileges
> > on the ctakes confluence site?
> >
> > There was a bug in the umls install; copy
> > https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> > ytex/scripts/data/build.xmlover
> > the corresponding file in your ctakes-3.1.2 install
> > (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set. The
> > import is currently running on the UMLS 2013AA (I assume this will
> complete
> > without issues as long as the umls schema hasn't changed from 2012).
> >
> > what trial and error did you have to go through to build the distro?
> >
> > -vj
> >
> >
> > On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> >
> > > Hi Vlad,
> > >
> > > sorry that the instructions aren't clear.
> > >
> > > re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot
> > > as usual (this is unchanged from 3.1.1). After that you still have to
> > > apply the lib and resources (these are things that cannot be
> > > distributed via apache).
> > >
> > > re 2) Yes, I need to update those docs. Hopefully will get to that at
> > > some point. However, I assume you already have a UMLS DB (also assume
> > > SQL Server). If you can't/don't want to use your existing umls DB,
> > > please tell me. The I'll priortize upgrading the doc on importing the
> > > umls tables (the scripts are there).
> > >
> > > best,
> > >
> > > VJ
> > >
> > >
> > > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> > >
> > >> Hi VJ-
> > >>
> > >> so, with trial and error were able to make the distribution and now
> > >> have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> > >>
> > >> Here's what's unclear.
> > >>
> > >> 1. Is now this the only (combined) thing that you need for ctakes
> > >> 3.1.1 + Ytex?
> > >> the current documentation (https://code.google.com/p/yte
> > >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> > >> lation_cTAKES_3_1)
> > >> which most probably is outdated, talks about installing cTakes 3.1.1
> > >> first and then applying 2 SNAPSHOT archives (downloadable) , lib and
> > >> resources.
> > >> This is a confusion point.
> > >>
> > >> 2. The directions to import UMLS subset are then outdated as well.
> > >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to
> > >> import the RRF files for the UMLS subset and then just use the
> > >> resulting db. Thoughts?
> > >>
> > >> Thanks,
> > >> Vlad Valtchinov
> > >> Brigham Rad
> > >>
> > >>
> > >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> > >>
> > >>> Hi Vlad,
> > >>>
> > >>>
> > >> All of ytex has been moved into ctakes, it is currently in a branch (
> > >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't
> > >>> have to install ytex-0.8 - instead you will have to build and
> > >>> install from the ytex branch to create your own distribution. Steps
> 2 & 3
> > are correct.
> > >>>
> > >>> Although it is a pain, if you have the jdk, maven, and svn, you can
> > >>> easily build your own distro:
> > >>> * open a command prompt
> > >>> * make sure jdk, maven, and svn are in your path
> > >>> * cd to some directory where you want to check stuff out (I like
> > >>> c:\temp)
> > >>> * run the following commands
> > >>> rmdir /s /q ctakes
> > >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
> > >>> cd ctakes mvn clean install -DskipTests
> > >>>
> > >>> And you will have the ctakes (with ytex) distro in
> > >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.z
> > >>> ip
> > >>>
> > >>> What is the process for getting the ytex branch merged into trunk?
> > >>> As I mentioned, there are very few changes to other ctakes
> > >>> classes/types - this should be completely complementary and not
> > >>> affect any existing ctakes functionality.
> > >>>
> > >>> -vj
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> > >>>
> > >>>> Hi VJ--
> > >>>>
> > >>>> this is great!! Thanks for all the hard work on it!
> > >>>>
> > >>>> We're starting to look into the new install. For now we're trying
> > >>>> the binaries out.
> > >>>>
> > >>>> There were these questions about the proper install steps:
> > >>>>
> > >>>> 1. Do we first install ytex-0.8
> > >>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
> > >>>> SNAPSHOT lib and resources zips 3. Work our way to install the UMLS
> > >>>> ontologies in the db
> > >>>>
> > >>>> Its is not entirely clear from the new document (
> > >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> > >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> > >>>> if there's still need to install ytex-0.8, or YTEX has been
> > >>>> entirely merged into cTakes?
> > >>>>
> > >>>> If the last statement is correct, there are missing parts in i.e
> > >>>> the UMLS install steps that are linked from the new ctakes 3.1.1
> > document.
> > >>>>
> > >>>> Thanks,
> > >>>> vlad
> > >>>>
> > >>>>
> > >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> > >>>>>
> > >>>>> Hello All,
> > >>>>>
> > >>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
> > >>>>> Most of the YTEX functionality has been ported and integrated
> > >>>>> with cTAKES, and I've tested with MySQL and MS SQL Server (oracle
> > tests pending).
> > >>>>>
> > >>>>> Most of the changes were made in new projects - very little
> > >>>>> existing cTAKES code has been modified. The only non-trivial
> > >>>>> changes are in
> > >>>>> /ctakes-
> > assertion/src/main/java/org/apache/ctakes/assertion/medfac
> > >>>>> ts/i2b2/api
> > >>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
> > >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> > >>>>> sentences correctly. Can somebody take a look at the changes in
> the
> > ytex branch?
> > >>>>>
> > >>>>> I believe that the branch https://svn.apache.org/
> > >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes
> > >>>>> trunk, but would like other users to test it as well. Questions:
> > >>>>>
> > >>>>> * How can I distribute the ctakes binary distribution to ytex
> > >>>>> users before the merge? Can we make the branch build available
> > >>>>> somewhere? The binary distribution is too large to host on the
> > >>>>> ytex google code site (max
> > >>>>> 200 MB)
> > >>>>> * Non-ASF libraries - I have segregated these out into their own
> > >>>>> zip file that can be distributed via sourceforge. As a stopgap, I
> > >>>>> can upload this to the ytex google code site, but would prefer to
> > >>>>> upload to sourceforge.
> > >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> > >>>>> sourceforge.
> > >>>>> * Documentation - How can I update the confluence docs? I would
> > >>>>> migrate the documentation from the google code website.
> > >>>>>
> > >>>>> Here the installation instructions (putting the wagon in front of
> > >>>>> the horse ...)
> > >>>>>
> > >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> > >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> > >>>>>
> > >>>>> Best,
> > >>>>>
> > >>>>> VJ
> > >>>>>
> > >>>>>
> > >>>>> --
> > >>>> You received this message because you are subscribed to the Google
> > >>>> Groups "ytex-users" group.
> > >>>> To unsubscribe from this group and stop receiving emails from it,
> > >>>> send an email to ytex-users+...@googlegroups.com.
> > >>>> To post to this group, send email to ytex-...@googlegroups.com.
> > >>>> To view this discussion on the web visit
> > >>>> https://groups.google.com/d/
> > >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> > >>>> 40googlegroups.com.
> > >>>>
> > >>>> For more options, visit https://groups.google.com/groups/opt_out.
> > >>>>
> > >>>
> > >>> --
> > >> You received this message because you are subscribed to the Google
> > >> Groups "ytex-users" group.
> > >> To unsubscribe from this group and stop receiving emails from it,
> > >> send an email to ytex-users+unsubscribe@googlegroups.com.
> > >> To post to this group, send email to ytex-users@googlegroups.com.
> > >> To view this discussion on the web visit
> > >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-
> > a273-
> > >> a3b1a7b36241%40googlegroups.com
> > >> .
> > >>
> > >> For more options, visit https://groups.google.com/groups/opt_out.
> > >>
> > >
> > >
>
RE: YTEX cTAKES 3.1.1 ready
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
VJ,
Aside from the changes to the existing cTAKES code (sentence detector, etc.) [which we could leave out if it's still being debated],
Do you think it's worth migrating the ytex code to trunk at this point? As you mentioned earlier, it's largely complementary.
[I was just thinking of saving effort to maintain the separate branch and for simplicity for dev...]
--Pei
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Wednesday, February 05, 2014 9:30 PM
> To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org;
> vlad.valtchinov@gmail.com
> Subject: Re: YTEX cTAKES 3.1.1 ready
>
> Hi Vlad,
>
> I Updated the umls install guide; see
> https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
>
> I would prefer to add the docs in the ctakes confluence, but as far as I can
> tell, I don't have write access there - can somebody give me write privileges
> on the ctakes confluence site?
>
> There was a bug in the umls install; copy
> https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-
> ytex/scripts/data/build.xmlover
> the corresponding file in your ctakes-3.1.2 install
> (CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set. The
> import is currently running on the UMLS 2013AA (I assume this will complete
> without issues as long as the umls schema hasn't changed from 2012).
>
> what trial and error did you have to go through to build the distro?
>
> -vj
>
>
> On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
>
> > Hi Vlad,
> >
> > sorry that the instructions aren't clear.
> >
> > re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot
> > as usual (this is unchanged from 3.1.1). After that you still have to
> > apply the lib and resources (these are things that cannot be
> > distributed via apache).
> >
> > re 2) Yes, I need to update those docs. Hopefully will get to that at
> > some point. However, I assume you already have a UMLS DB (also assume
> > SQL Server). If you can't/don't want to use your existing umls DB,
> > please tell me. The I'll priortize upgrading the doc on importing the
> > umls tables (the scripts are there).
> >
> > best,
> >
> > VJ
> >
> >
> > On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
> >
> >> Hi VJ-
> >>
> >> so, with trial and error were able to make the distribution and now
> >> have the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
> >>
> >> Here's what's unclear.
> >>
> >> 1. Is now this the only (combined) thing that you need for ctakes
> >> 3.1.1 + Ytex?
> >> the current documentation (https://code.google.com/p/yte
> >> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
> >> lation_cTAKES_3_1)
> >> which most probably is outdated, talks about installing cTakes 3.1.1
> >> first and then applying 2 SNAPSHOT archives (downloadable) , lib and
> >> resources.
> >> This is a confusion point.
> >>
> >> 2. The directions to import UMLS subset are then outdated as well.
> >> Maybe one should use the old version (ctakes 2.5 and ytex 0.8) to
> >> import the RRF files for the UMLS subset and then just use the
> >> resulting db. Thoughts?
> >>
> >> Thanks,
> >> Vlad Valtchinov
> >> Brigham Rad
> >>
> >>
> >> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
> >>
> >>> Hi Vlad,
> >>>
> >>>
> >> All of ytex has been moved into ctakes, it is currently in a branch (
> >>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't
> >>> have to install ytex-0.8 - instead you will have to build and
> >>> install from the ytex branch to create your own distribution. Steps 2 & 3
> are correct.
> >>>
> >>> Although it is a pain, if you have the jdk, maven, and svn, you can
> >>> easily build your own distro:
> >>> * open a command prompt
> >>> * make sure jdk, maven, and svn are in your path
> >>> * cd to some directory where you want to check stuff out (I like
> >>> c:\temp)
> >>> * run the following commands
> >>> rmdir /s /q ctakes
> >>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
> >>> cd ctakes mvn clean install -DskipTests
> >>>
> >>> And you will have the ctakes (with ytex) distro in
> >>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.z
> >>> ip
> >>>
> >>> What is the process for getting the ytex branch merged into trunk?
> >>> As I mentioned, there are very few changes to other ctakes
> >>> classes/types - this should be completely complementary and not
> >>> affect any existing ctakes functionality.
> >>>
> >>> -vj
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
> >>>
> >>>> Hi VJ--
> >>>>
> >>>> this is great!! Thanks for all the hard work on it!
> >>>>
> >>>> We're starting to look into the new install. For now we're trying
> >>>> the binaries out.
> >>>>
> >>>> There were these questions about the proper install steps:
> >>>>
> >>>> 1. Do we first install ytex-0.8
> >>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
> >>>> SNAPSHOT lib and resources zips 3. Work our way to install the UMLS
> >>>> ontologies in the db
> >>>>
> >>>> Its is not entirely clear from the new document (
> >>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
> >>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
> >>>> if there's still need to install ytex-0.8, or YTEX has been
> >>>> entirely merged into cTakes?
> >>>>
> >>>> If the last statement is correct, there are missing parts in i.e
> >>>> the UMLS install steps that are linked from the new ctakes 3.1.1
> document.
> >>>>
> >>>> Thanks,
> >>>> vlad
> >>>>
> >>>>
> >>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
> >>>>>
> >>>>> Hello All,
> >>>>>
> >>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
> >>>>> Most of the YTEX functionality has been ported and integrated
> >>>>> with cTAKES, and I've tested with MySQL and MS SQL Server (oracle
> tests pending).
> >>>>>
> >>>>> Most of the changes were made in new projects - very little
> >>>>> existing cTAKES code has been modified. The only non-trivial
> >>>>> changes are in
> >>>>> /ctakes-
> assertion/src/main/java/org/apache/ctakes/assertion/medfac
> >>>>> ts/i2b2/api
> >>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
> >>>>> SingleDocumentProcessorCtakes to deal with newlines within
> >>>>> sentences correctly. Can somebody take a look at the changes in the
> ytex branch?
> >>>>>
> >>>>> I believe that the branch https://svn.apache.org/
> >>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes
> >>>>> trunk, but would like other users to test it as well. Questions:
> >>>>>
> >>>>> * How can I distribute the ctakes binary distribution to ytex
> >>>>> users before the merge? Can we make the branch build available
> >>>>> somewhere? The binary distribution is too large to host on the
> >>>>> ytex google code site (max
> >>>>> 200 MB)
> >>>>> * Non-ASF libraries - I have segregated these out into their own
> >>>>> zip file that can be distributed via sourceforge. As a stopgap, I
> >>>>> can upload this to the ytex google code site, but would prefer to
> >>>>> upload to sourceforge.
> >>>>> * UMLS Derivatives - Ditto for these - would like to move to
> >>>>> sourceforge.
> >>>>> * Documentation - How can I update the confluence docs? I would
> >>>>> migrate the documentation from the google code website.
> >>>>>
> >>>>> Here the installation instructions (putting the wagon in front of
> >>>>> the horse ...)
> >>>>>
> >>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
> >>>>> ts=1388793998&updated=Installation_cTAKES_3_1
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> VJ
> >>>>>
> >>>>>
> >>>>> --
> >>>> You received this message because you are subscribed to the Google
> >>>> Groups "ytex-users" group.
> >>>> To unsubscribe from this group and stop receiving emails from it,
> >>>> send an email to ytex-users+...@googlegroups.com.
> >>>> To post to this group, send email to ytex-...@googlegroups.com.
> >>>> To view this discussion on the web visit
> >>>> https://groups.google.com/d/
> >>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
> >>>> 40googlegroups.com.
> >>>>
> >>>> For more options, visit https://groups.google.com/groups/opt_out.
> >>>>
> >>>
> >>> --
> >> You received this message because you are subscribed to the Google
> >> Groups "ytex-users" group.
> >> To unsubscribe from this group and stop receiving emails from it,
> >> send an email to ytex-users+unsubscribe@googlegroups.com.
> >> To post to this group, send email to ytex-users@googlegroups.com.
> >> To view this discussion on the web visit
> >> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-
> a273-
> >> a3b1a7b36241%40googlegroups.com
> >> .
> >>
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>
> >
> >
RE: YTEX cTAKES 3.1.1 ready
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Hi Vijay,
I gave you write access to the cTAKES space on the confluence site
-- James
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Wednesday, February 05, 2014 8:29 PM
To: ytex-users@googlegroups.com; ctakes-dev@incubator.apache.org; vlad.valtchinov@gmail.com
Subject: Re: YTEX cTAKES 3.1.1 ready
Hi Vlad,
I Updated the umls install guide; see
https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
I would prefer to add the docs in the ctakes confluence, but as far as I
can tell, I don't have write access there - can somebody give me write
privileges on the ctakes confluence site?
There was a bug in the umls install; copy
https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xmlover
the corresponding file in your ctakes-3.1.2 install
(CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set. The
import is currently running on the UMLS 2013AA (I assume this will complete
without issues as long as the umls schema hasn't changed from 2012).
what trial and error did you have to go through to build the distro?
-vj
On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> Hi Vlad,
>
> sorry that the instructions aren't clear.
>
> re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot as
> usual (this is unchanged from 3.1.1). After that you still have to apply
> the lib and resources (these are things that cannot be distributed via
> apache).
>
> re 2) Yes, I need to update those docs. Hopefully will get to that at
> some point. However, I assume you already have a UMLS DB (also assume SQL
> Server). If you can't/don't want to use your existing umls DB, please tell
> me. The I'll priortize upgrading the doc on importing the umls tables (the
> scripts are there).
>
> best,
>
> VJ
>
>
> On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
>
>> Hi VJ-
>>
>> so, with trial and error were able to make the distribution and now have
>> the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
>>
>> Here's what's unclear.
>>
>> 1. Is now this the only (combined) thing that you need for ctakes 3.1.1 +
>> Ytex?
>> the current documentation (https://code.google.com/p/yte
>> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
>> lation_cTAKES_3_1)
>> which most probably is outdated, talks about installing cTakes 3.1.1
>> first and then applying 2 SNAPSHOT archives (downloadable) , lib and
>> resources.
>> This is a confusion point.
>>
>> 2. The directions to import UMLS subset are then outdated as well. Maybe
>> one should use the old version (ctakes 2.5 and ytex 0.8) to
>> import the RRF files for the UMLS subset and then just use the resulting
>> db. Thoughts?
>>
>> Thanks,
>> Vlad Valtchinov
>> Brigham Rad
>>
>>
>> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
>>
>>> Hi Vlad,
>>>
>>>
>> All of ytex has been moved into ctakes, it is currently in a branch (
>>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't have
>>> to install ytex-0.8 - instead you will have to build and install from the
>>> ytex branch to create your own distribution. Steps 2 & 3 are correct.
>>>
>>> Although it is a pain, if you have the jdk, maven, and svn, you can
>>> easily build your own distro:
>>> * open a command prompt
>>> * make sure jdk, maven, and svn are in your path
>>> * cd to some directory where you want to check stuff out (I like c:\temp)
>>> * run the following commands
>>> rmdir /s /q ctakes
>>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
>>> cd ctakes
>>> mvn clean install -DskipTests
>>>
>>> And you will have the ctakes (with ytex) distro in
>>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.zip
>>>
>>> What is the process for getting the ytex branch merged into trunk? As I
>>> mentioned, there are very few changes to other ctakes classes/types - this
>>> should be completely complementary and not affect any existing ctakes
>>> functionality.
>>>
>>> -vj
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
>>>
>>>> Hi VJ--
>>>>
>>>> this is great!! Thanks for all the hard work on it!
>>>>
>>>> We're starting to look into the new install. For now we're trying the
>>>> binaries out.
>>>>
>>>> There were these questions about the proper install steps:
>>>>
>>>> 1. Do we first install ytex-0.8
>>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
>>>> SNAPSHOT lib and resources zips
>>>> 3. Work our way to install the UMLS ontologies in the db
>>>>
>>>> Its is not entirely clear from the new document (
>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
>>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
>>>> if there's still need to install ytex-0.8, or YTEX has been entirely
>>>> merged into cTakes?
>>>>
>>>> If the last statement is correct, there are missing parts in i.e the
>>>> UMLS install steps that are linked from the new ctakes 3.1.1 document.
>>>>
>>>> Thanks,
>>>> vlad
>>>>
>>>>
>>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
>>>>>
>>>>> Hello All,
>>>>>
>>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
>>>>> Most of the YTEX functionality has been ported and integrated with cTAKES,
>>>>> and I've tested with MySQL and MS SQL Server (oracle tests pending).
>>>>>
>>>>> Most of the changes were made in new projects - very little existing
>>>>> cTAKES code has been modified. The only non-trivial changes are
>>>>> in /ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api
>>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
>>>>> SingleDocumentProcessorCtakes to deal with newlines within sentences
>>>>> correctly. Can somebody take a look at the changes in the ytex branch?
>>>>>
>>>>> I believe that the branch https://svn.apache.org/
>>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes
>>>>> trunk, but would like other users to test it as well. Questions:
>>>>>
>>>>> * How can I distribute the ctakes binary distribution to ytex users
>>>>> before the merge? Can we make the branch build available somewhere? The
>>>>> binary distribution is too large to host on the ytex google code site (max
>>>>> 200 MB)
>>>>> * Non-ASF libraries - I have segregated these out into their own zip
>>>>> file that can be distributed via sourceforge. As a stopgap, I can upload
>>>>> this to the ytex google code site, but would prefer to upload to
>>>>> sourceforge.
>>>>> * UMLS Derivatives - Ditto for these - would like to move to
>>>>> sourceforge.
>>>>> * Documentation - How can I update the confluence docs? I would
>>>>> migrate the documentation from the google code website.
>>>>>
>>>>> Here the installation instructions (putting the wagon in front of the
>>>>> horse ...)
>>>>>
>>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
>>>>> ts=1388793998&updated=Installation_cTAKES_3_1
>>>>>
>>>>> Best,
>>>>>
>>>>> VJ
>>>>>
>>>>>
>>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "ytex-users" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to ytex-users+...@googlegroups.com.
>>>> To post to this group, send email to ytex-...@googlegroups.com.
>>>> To view this discussion on the web visit https://groups.google.com/d/
>>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
>>>> 40googlegroups.com.
>>>>
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "ytex-users" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to ytex-users+unsubscribe@googlegroups.com.
>> To post to this group, send email to ytex-users@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-a273-a3b1a7b36241%40googlegroups.com
>> .
>>
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>
Re: YTEX cTAKES 3.1.1 ready
Posted by vijay garla <vn...@gmail.com>.
Hi Vlad,
I Updated the umls install guide; see
https://code.google.com/p/ytex/wiki/UMLS_SQL_SERVER_3_1
I would prefer to add the docs in the ctakes confluence, but as far as I
can tell, I don't have write access there - can somebody give me write
privileges on the ctakes confluence site?
There was a bug in the umls install; copy
https://svn.apache.org/repos/asf/ctakes/branches/ytex/ctakes-ytex/scripts/data/build.xmlover
the corresponding file in your ctakes-3.1.2 install
(CTAKES_HOME\bin\ctakes-ytex\scripts\data) and you should be set. The
import is currently running on the UMLS 2013AA (I assume this will complete
without issues as long as the umls schema hasn't changed from 2012).
what trial and error did you have to go through to build the distro?
-vj
On Wed, Feb 5, 2014 at 5:33 PM, vijay garla <vn...@gmail.com> wrote:
> Hi Vlad,
>
> sorry that the instructions aren't clear.
>
> re 1) What I am trying to say is install apache-ctakes-3.2.0-snapshot as
> usual (this is unchanged from 3.1.1). After that you still have to apply
> the lib and resources (these are things that cannot be distributed via
> apache).
>
> re 2) Yes, I need to update those docs. Hopefully will get to that at
> some point. However, I assume you already have a UMLS DB (also assume SQL
> Server). If you can't/don't want to use your existing umls DB, please tell
> me. The I'll priortize upgrading the doc on importing the umls tables (the
> scripts are there).
>
> best,
>
> VJ
>
>
> On Wed, Feb 5, 2014 at 4:44 PM, <vl...@gmail.com> wrote:
>
>> Hi VJ-
>>
>> so, with trial and error were able to make the distribution and now have
>> the apache-ctakes-3.1.2-SNAPSHOT-bin.zip archive.
>>
>> Here's what's unclear.
>>
>> 1. Is now this the only (combined) thing that you need for ctakes 3.1.1 +
>> Ytex?
>> the current documentation (https://code.google.com/p/yte
>> x/wiki/Installation_cTAKES_3_1?ts=1388793998&updated=Instal
>> lation_cTAKES_3_1)
>> which most probably is outdated, talks about installing cTakes 3.1.1
>> first and then applying 2 SNAPSHOT archives (downloadable) , lib and
>> resources.
>> This is a confusion point.
>>
>> 2. The directions to import UMLS subset are then outdated as well. Maybe
>> one should use the old version (ctakes 2.5 and ytex 0.8) to
>> import the RRF files for the UMLS subset and then just use the resulting
>> db. Thoughts?
>>
>> Thanks,
>> Vlad Valtchinov
>> Brigham Rad
>>
>>
>> On Thursday, January 30, 2014 5:17:43 PM UTC-5, vijay garla wrote:
>>
>>> Hi Vlad,
>>>
>>>
>> All of ytex has been moved into ctakes, it is currently in a branch (
>>> https://svn.apache.org/repos/asf/ctakes/branches/ytex). You don't have
>>> to install ytex-0.8 - instead you will have to build and install from the
>>> ytex branch to create your own distribution. Steps 2 & 3 are correct.
>>>
>>> Although it is a pain, if you have the jdk, maven, and svn, you can
>>> easily build your own distro:
>>> * open a command prompt
>>> * make sure jdk, maven, and svn are in your path
>>> * cd to some directory where you want to check stuff out (I like c:\temp)
>>> * run the following commands
>>> rmdir /s /q ctakes
>>> svn co https://svn.apache.org/repos/asf/ctakes/branches/ytex ctakes
>>> cd ctakes
>>> mvn clean install -DskipTests
>>>
>>> And you will have the ctakes (with ytex) distro in
>>> ctakes\ctakes-distribution\target\apache-ctakes-3.1.2-SNAPSHOT-bin.zip
>>>
>>> What is the process for getting the ytex branch merged into trunk? As I
>>> mentioned, there are very few changes to other ctakes classes/types - this
>>> should be completely complementary and not affect any existing ctakes
>>> functionality.
>>>
>>> -vj
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Jan 30, 2014 at 4:56 PM, <vl...@gmail.com> wrote:
>>>
>>>> Hi VJ--
>>>>
>>>> this is great!! Thanks for all the hard work on it!
>>>>
>>>> We're starting to look into the new install. For now we're trying the
>>>> binaries out.
>>>>
>>>> There were these questions about the proper install steps:
>>>>
>>>> 1. Do we first install ytex-0.8
>>>> 2. Then install the new cTakes 3.1.1 instance and also apply the
>>>> SNAPSHOT lib and resources zips
>>>> 3. Work our way to install the UMLS ontologies in the db
>>>>
>>>> Its is not entirely clear from the new document (
>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_
>>>> 1?ts=1388793998&updated=Installation_cTAKES_3_1)
>>>> if there's still need to install ytex-0.8, or YTEX has been entirely
>>>> merged into cTakes?
>>>>
>>>> If the last statement is correct, there are missing parts in i.e the
>>>> UMLS install steps that are linked from the new ctakes 3.1.1 document.
>>>>
>>>> Thanks,
>>>> vlad
>>>>
>>>>
>>>> On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
>>>>>
>>>>> Hello All,
>>>>>
>>>>> I have finished an initial cut at the port of YTEX to cTAKES 3.1.1.
>>>>> Most of the YTEX functionality has been ported and integrated with cTAKES,
>>>>> and I've tested with MySQL and MS SQL Server (oracle tests pending).
>>>>>
>>>>> Most of the changes were made in new projects - very little existing
>>>>> cTAKES code has been modified. The only non-trivial changes are
>>>>> in /ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api
>>>>> - here I modified CharacterOffsetToLineTokenConverterCtakesImpl &
>>>>> SingleDocumentProcessorCtakes to deal with newlines within sentences
>>>>> correctly. Can somebody take a look at the changes in the ytex branch?
>>>>>
>>>>> I believe that the branch https://svn.apache.org/
>>>>> repos/asf/ctakes/branches/ytex is ready to be merged into ctakes
>>>>> trunk, but would like other users to test it as well. Questions:
>>>>>
>>>>> * How can I distribute the ctakes binary distribution to ytex users
>>>>> before the merge? Can we make the branch build available somewhere? The
>>>>> binary distribution is too large to host on the ytex google code site (max
>>>>> 200 MB)
>>>>> * Non-ASF libraries - I have segregated these out into their own zip
>>>>> file that can be distributed via sourceforge. As a stopgap, I can upload
>>>>> this to the ytex google code site, but would prefer to upload to
>>>>> sourceforge.
>>>>> * UMLS Derivatives - Ditto for these - would like to move to
>>>>> sourceforge.
>>>>> * Documentation - How can I update the confluence docs? I would
>>>>> migrate the documentation from the google code website.
>>>>>
>>>>> Here the installation instructions (putting the wagon in front of the
>>>>> horse ...)
>>>>>
>>>>> https://code.google.com/p/ytex/wiki/Installation_cTAKES_3_1?
>>>>> ts=1388793998&updated=Installation_cTAKES_3_1
>>>>>
>>>>> Best,
>>>>>
>>>>> VJ
>>>>>
>>>>>
>>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "ytex-users" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to ytex-users+...@googlegroups.com.
>>>> To post to this group, send email to ytex-...@googlegroups.com.
>>>> To view this discussion on the web visit https://groups.google.com/d/
>>>> msgid/ytex-users/70f03a80-ce1a-4c0e-b35d-5116d1c93ea0%
>>>> 40googlegroups.com.
>>>>
>>>> For more options, visit https://groups.google.com/groups/opt_out.
>>>>
>>>
>>> --
>> You received this message because you are subscribed to the Google Groups
>> "ytex-users" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to ytex-users+unsubscribe@googlegroups.com.
>> To post to this group, send email to ytex-users@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/ytex-users/bc3bd705-55d2-4acd-a273-a3b1a7b36241%40googlegroups.com
>> .
>>
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
>