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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Preparing for an Apache cTAKES 3.2 Release?
Date Wed, 11 Jun 2014 13:56:23 GMT
> it would be incredibly helpful to have thorough documentation

I agree.  There is some documentation in the module's doc/ directory, but it is very brief.
 There are also some example descriptors in the example/ directory.  The -resource also has
some example xmls and dictionaries.

It isn't much, but I have a small plate heaped with large portions of many courses and very
little time to document.  If there are questions please write me and I'll update the documentation
as necessary.  Anybody else that feels inclined can also add to the docs.  Eventually the
documentation should be moved to reside with the rest of the cTakes docs.

Sean

-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com] 
Sent: Wednesday, June 11, 2014 9:33 AM
To: dev@ctakes.apache.org
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

regardless of the name, I think it would be incredibly helpful to have thorough documentation
on the dictionary lookup, how to configure it, and how to create new dictionaries.  I would
venture to say that this is the most important component in cTAKES, and probably the one that
has generated the most questions on the newsgroup.



On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> >. The newer NER should have in its name the Behavior...
>
> I agree, but the *2 module is a complete replacement for the current 
> lookup.  It does not (really) have any different behavior, just a 
> different implementation and performance.  We plan to swap out the old 
> with the new in the next release and get rid of the *2 suffix.  So, 
> any name provided now is just temporary - unless people don't like the 
> name "dictionary-lookup" at all.
>
> In my original sandbox it was named "RareWordLookup", a nod to its 
> implementation.  However, this doesn't help any users.
>
> Sean
>
> -----Original Message-----
> From: andy mcmurry [mailto:mcmurry.andy@gmail.com]
> Sent: Wednesday, June 11, 2014 3:09 AM
> To: dev@ctakes.apache.org
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>
> "2" doesn't mean much. The newer NER should have in its name the 
> Behavior...
>
> Perhaps something like MetaMap Usage
> <http://metamap.nlm.nih.gov/Docs/MM09_Usage.shtml> "--allow_overmatches"
> or  "--allow_concept_gaps" or .....other?
>
> Since yTex already provides a pluggable *DictionaryLookup, *that seems 
> like the best place to define the differing Behavior /  Usage.
>
> https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
> https://code.google.com/p/ytex/wiki/DictionaryLookup_V05
>
>
> AndyMC
>
> On Tue, Jun 10, 2014 at 9:55 AM, britt fitch <britt.fitch@gmail.com>
> wrote:
>
> > I don’t have an issue with the *-2 name. I also don’t have any 
> > objections to renaming it.
> >
> > It might be nice to keep the old dictionary code around for a 
> > release-worth of time but after that I would vote purging it.
> > If someone needs it after that it’ll be accessible in the archived 
> > releases.
> >
> >
> >
> > On Jun 10, 2014, at 12:48 PM, Chen, Pei 
> > <Pei.Chen@childrens.harvard.edu>
> > wrote:
> >
> > > I think James has a fair point here.
> > > It may be worthwhile biting the bullet here and push forward.
> > >
> > > Since this essentially will be a full replacement of the
> > ctakes-dictionary-lookup module, a good option maybe to just replace 
> > the entire module now and rename the existing module to * _deprecated.
> > > How do folks feel about that?  In a nutshell,
> > > ctakes-dictionary-lookup-2
> > is a faster algorithm with a simpler code base- and comparable 
> > results (Sean has a full comparison in the documentation for those 
> > who are
> curious).
> > >
> > > --Pei
> > >
> > >> -----Original Message-----
> > >> From: britt fitch [mailto:britt.fitch@gmail.com]
> > >> Sent: Monday, June 09, 2014 5:42 PM
> > >> To: dev@ctakes.apache.org
> > >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>
> > >> There is some documentation in the dictionary2 module under 
> > >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some 
> > >> details of
> > the
> > >> different lookup implementation options within that module that I 
> > >> found helpful.
> > >>
> > >>
> > >> On Jun 9, 2014, at 5:17 PM, Masanz, James J.
> > >> <Masanz.James@mayo.edu>
> > >> wrote:
> > >>
> > >>>
> > >>> Will ctakes-dictionary-lookup2 remain the name for the new 
> > >>> dictionary
> > >> lookup or will it have a name that reflects the algorithm?
> > >>>
> > >>> Is there a description of it that will help users to decide when 
> > >>> to
> > use one
> > >> dictionary lookup component vs. the other.
> > >>>
> > >>> -- James
> > >>>
> > >>> -----Original Message-----
> > >>> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> > >>> Sent: Friday, June 06, 2014 12:34 PM
> > >>> To: dev@ctakes.apache.org
> > >>> Subject: Preparing for an Apache cTAKES 3.2 Release?
> > >>>
> > >>> Hi,
> > >>> The 3.2 release was slated to be release end of this month (Jun 21).
> > >>> Since I volunteered to be the RM for this release, just like the 
> > >>> past
> > >> releases, I was planning to create a branch/tag next week from 
> > >> trunk and dev can continue.
> > >>> Feel free to take a look at any outstanding Jira issues [1] that 
> > >>> you
> > may want
> > >> to be included in this release.
> > >>>
> > >>> Major changes include:
> > >>> CTAKES-197        Upgrade cTAKES to Java 7
> > >>> CTAKES-292        Integrate YTEX with cTAKES
> > >>> CTAKES-82          Add ctakes-temporal module (Time and Event
> > Annotator +
> > >> DocTimeRel Property only?)
> > >>>
> > >>> [1]
> > >>> https://issues.apache.org/jira/browse/CTAKES-
> > >> 298?jql=fixVersion%20%3D%
> > >>> 203.2.0%20AND%20project%20%3D%20CTAKES
> > >>>
> > >>>> -----Original Message-----
> > >>>> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> > >>>> Sent: Wednesday, March 26, 2014 9:34 PM
> > >>>> To: 'dev@ctakes.apache.org'
> > >>>> Subject: RE: Apache cTAKES 3.2 Release?
> > >>>>
> > >>>> +1 to naming it 3.2
> > >>>>
> > >>>> I'll review my JIRA items this week.
> > >>>>
> > >>>> -- James
> > >>>>
> > >>>> -----Original Message-----
> > >>>> From: Pei Chen [mailto:chenpei@apache.org]
> > >>>> Sent: Wednesday, March 26, 2014 10:14 AM
> > >>>> To: dev@ctakes.apache.org
> > >>>> Subject: Apache cTAKES 3.2 Release?
> > >>>>
> > >>>> Hi,
> > >>>>
> > >>>> I think there are a lot of items slated for the next release, I

> > >>>> suggest we make it 3.2 instead of another patch release.
> > >>>>
> > >>>> I can volunteer to be the RM unless someone would like to take

> > >>>> that
> > up...
> > >>>>
> > >>>>
> > >>>>
> > >>>> Main Changes pending for 3.2:
> > >>>>
> > >>>> CTAKES-197        Upgrade cTAKES to Java 7
> > >>>>
> > >>>> CTAKES-292        Integrate YTEX with cTAKES
> > >>>>
> > >>>> CTAKES-82          Add ctakes-temporal module (Time and Event
> > Annotator
> > >> +
> > >>>> DocTimeRel Property only?)
> > >>>>
> > >>>> CTAKES-275        some of the older junit tests don't have the
right
> > >>>> Project name in the run configurations
> > >>>>
> > >>>> CTAKES-268        Fix SentenceDetector training with updated OpenNLP
> > API
> > >>>>
> > >>>> CTAKES-162        Command line scripts leave the user back one
> > directory
> > >>>>
> > >>>> CTAKES-241        NullPointerException in ctakes-assertion
> > >>>>
> > >>>> CTAKES-288        Severity not set for DiseaseDisorderMention
> > >>>>
> > >>>> CTAKES-239        Medication Modifiers do not have the offsets
> > populated
> > >>>>
> > >>>> CTAKES-94          refactoring assertion module to use a
> cleartk-based
> > >>>> analysis engine (and include evaluation)
> > >>>>
> > >>>> CTAKES-232        change concept type
> > >>>>
> > >>>> CTAKES-76          get third party dependencies into Maven Central
> > >>>>
> > >>>> CTAKES-138        Remove 3rd party jars from our SVN
> > >>>>
> > >>>> CTAKES-74          Tokenizer PennTreeBank breaks with certain
> > apostrophes
> > >>>> in tokens.
> > >>>>
> > >>>> CTAKES-225        Common Type System - Add field to save
> > preferredText in
> > >>>> Segment
> > >>>>
> > >>>> CTAKES-222        FirstTokenPermLookupInitializerImpl to suppot
> > arraylist
> > >>>> of DictionaryLookupWindows
> > >>>>
> > >>>> CTAKES-213        ModifierExtractorAnnotator should produce
> > XxxxModifier
> > >>>> subtypes
> > >>>>
> > >>>>
> > >>>>
> > >>>> Full List:
> > >>>>
> > >>>> https://issues.apache.org/jira/browse/CTAKES-
> > >>>>
> > >> 288?jql=project%20%3D%20CTAKES%20AND%20fixVersion%20%3D%203.2%
> > >>>>
> > >> 20ORDER%20BY%20updated%20DESC%2C%20priority%20DESC%2C%20create
> > >>>> d%20ASC
> > >
> >
> >
>
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