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From vijay garla <vnga...@gmail.com>
Subject Re: YTEX cTAKES 3.1.1 ready
Date Thu, 06 Feb 2014 15:30:23 GMT
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
<Pei.Chen@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 <vngarla@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, <vlad.valtchinov@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, <vlad.va...@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
> > >>>>>
> > >>>>>
> > >>>>>  --
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> > >
> > >
>

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