RE: Preparing for an Apache cTAKES 3.2 Release?

[Chen, Pei]

Renamed to *-fast.  
Again, this is only temporary... this will eventually just replace the existing 
dictionary lookup (next minor release?).

> -Original Message-
> From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
> Sent: Tuesday, June 17, 2014 10:14 AM
> To: dev@ctakes.apache.org
> Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> 
> Yes.  It's only temporary to give folks a chance try out and transition to the
> new lookup algorithm (hence, the +1 for the -fast suffix rename).
> But open to biting the bullet and defaulting it now if folks are compelled to
> do so.
> 
> > -Original Message-
> > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> > Sent: Monday, June 16, 2014 11:36 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> >
> > I guess that I've got one question at this point:
> >
> > Is the name being given to the -new- dictionary lookup module
> > temporary or permanent?
> >
> > I was under the assumption that it was temporary and that with the
> > switch to it being default (and eventually only) the module would
> > simply be named "dictionary-lookup".
> >
> >
> >
> > -Original Message-----
> > From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
> > Sent: Monday, June 16, 2014 11:24 AM
> > To: 'dev@ctakes.apache.org'
> > Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> >
> > I'd rather something else than "dictionary-lookup-fast". If we come up
> > with something even faster than this one, having an older one called
> > "fast" could be confusing.
> >
> > -Original Message-
> > From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
> > Sent: Monday, June 16, 2014 9:55 AM
> > To: cTAKES Developer list
> > Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >
> > +1
> >
> > Dima
> >
> >
> >
> >
> > On Jun 16, 2014, at 9:42, Miller, Timothy
> >  wrote:
> >
> > > Sorry to weigh in so late on this -- just returned from vacation. If
> > > we want to have a one release delay before making dictionary2
> > > default for testing/documentation/configuration purposes, and there
> > > isn't an obvious function-related name, and the main difference is
> > > speed, maybe we could call it dictionary-lookup-fast? Besides being
> > > accurate and more descriptive than "2", it might lure people into
> > > trying it and give us some feedback.
> > >
> > > Tim
> > >
> > >
> > > On 06/16/2014 10:34 AM, Chen, Pei wrote:
> > >> I'm making some significant updates to trunk that may cause some
> > instability for this release.
> > >> It should be mostly transparent, but let me know if you encounter
> > >> any
> > issues with trunk.
> > >>
> > >> Also, regarding the dictionary-lookup2.  If there are no strong
> > >> objections,
> > we can leave default to as-is (old behavior).  Folks who wish to give
> > the new one a try are welcome to do so and we can change the default
> > behavior in a future release.
> > >>
> > >> [ducks for cover now]
> > >> --Pei
> > >>
> > >>> -Original Message-
> > >>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of
> > >>> Karthik Sarma
> > >>> Sent: Wednesday, June 11, 2014 9:58 AM
> > >>> To: dev@ctakes.apache.org
> > >>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>>
> > >>> Agreed
> > >>>
> > >>> On Wednesday, June 11, 2014, vijay garla  wrote:
> > >>>
> > >>>> 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.fi...@childrens.harvard.edu> wrote:
> > >>>>
> > >>>>>> . The newer

RE: Preparing for an Apache cTAKES 3.2 Release?

[Chen, Pei]

Yes.  It's only temporary to give folks a chance try out and transition to the 
new lookup algorithm (hence, the +1 for the -fast suffix rename).
But open to biting the bullet and defaulting it now if folks are compelled to 
do so.

> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Monday, June 16, 2014 11:36 AM
> To: dev@ctakes.apache.org
> Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> 
> I guess that I've got one question at this point:
> 
> Is the name being given to the -new- dictionary lookup module temporary or
> permanent?
> 
> I was under the assumption that it was temporary and that with the switch to
> it being default (and eventually only) the module would simply be named
> "dictionary-lookup".
> 
> 
> 
> -Original Message-
> From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
> Sent: Monday, June 16, 2014 11:24 AM
> To: 'dev@ctakes.apache.org'
> Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> 
> I'd rather something else than "dictionary-lookup-fast". If we come up with
> something even faster than this one, having an older one called "fast" could
> be confusing.
> 
> -Original Message-
> From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
> Sent: Monday, June 16, 2014 9:55 AM
> To: cTAKES Developer list
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> 
> +1
> 
> Dima
> 
> 
> 
> 
> On Jun 16, 2014, at 9:42, Miller, Timothy
>  wrote:
> 
> > Sorry to weigh in so late on this -- just returned from vacation. If
> > we want to have a one release delay before making dictionary2 default
> > for testing/documentation/configuration purposes, and there isn't an
> > obvious function-related name, and the main difference is speed, maybe
> > we could call it dictionary-lookup-fast? Besides being accurate and
> > more descriptive than "2", it might lure people into trying it and
> > give us some feedback.
> >
> > Tim
> >
> >
> > On 06/16/2014 10:34 AM, Chen, Pei wrote:
> >> I'm making some significant updates to trunk that may cause some
> instability for this release.
> >> It should be mostly transparent, but let me know if you encounter any
> issues with trunk.
> >>
> >> Also, regarding the dictionary-lookup2.  If there are no strong objections,
> we can leave default to as-is (old behavior).  Folks who wish to give the new
> one a try are welcome to do so and we can change the default behavior in a
> future release.
> >>
> >> [ducks for cover now]
> >> --Pei
> >>
> >>> -Original Message-
> >>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of
> >>> Karthik Sarma
> >>> Sent: Wednesday, June 11, 2014 9:58 AM
> >>> To: dev@ctakes.apache.org
> >>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >>>
> >>> Agreed
> >>>
> >>> On Wednesday, June 11, 2014, vijay garla  wrote:
> >>>
> >>>> 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.fi...@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.
> >>>>>
> >>&

RE: Preparing for an Apache cTAKES 3.2 Release?

[Finan, Sean]

I guess that I've got one question at this point:

Is the name being given to the -new- dictionary lookup module temporary or 
permanent?  

I was under the assumption that it was temporary and that with the switch to it 
being default (and eventually only) the module would simply be named 
"dictionary-lookup".



-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] 
Sent: Monday, June 16, 2014 11:24 AM
To: 'dev@ctakes.apache.org'
Subject: RE: Preparing for an Apache cTAKES 3.2 Release?

I'd rather something else than "dictionary-lookup-fast". If we come up with 
something even faster than this one, having an older one called "fast" could be 
confusing.

-Original Message-
From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu]
Sent: Monday, June 16, 2014 9:55 AM
To: cTAKES Developer list
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

+1

Dima




On Jun 16, 2014, at 9:42, Miller, Timothy 
 wrote:

> Sorry to weigh in so late on this -- just returned from vacation. If 
> we want to have a one release delay before making dictionary2 default 
> for testing/documentation/configuration purposes, and there isn't an 
> obvious function-related name, and the main difference is speed, maybe 
> we could call it dictionary-lookup-fast? Besides being accurate and 
> more descriptive than "2", it might lure people into trying it and 
> give us some feedback.
> 
> Tim
> 
> 
> On 06/16/2014 10:34 AM, Chen, Pei wrote:
>> I'm making some significant updates to trunk that may cause some instability 
>> for this release.
>> It should be mostly transparent, but let me know if you encounter any issues 
>> with trunk.
>> 
>> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
>> we can leave default to as-is (old behavior).  Folks who wish to give the 
>> new one a try are welcome to do so and we can change the default behavior in 
>> a future release.
>> 
>> [ducks for cover now]
>> --Pei
>> 
>>> -Original Message-----
>>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of 
>>> Karthik Sarma
>>> Sent: Wednesday, June 11, 2014 9:58 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>> 
>>> Agreed
>>> 
>>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>> 
>>>> 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.fi...@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.a...@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 
>>

Re: Preparing for an Apache cTAKES 3.2 Release?

[Miller, Timothy]

I guess I saw it as a short-term thing -- having default and -fast, and
then if/when we deprecate the older one the -fast will just change to
regular ctakes-dictionary-lookup. But that could maybe be confusing to
people too.
Tim

On 06/16/2014 11:24 AM, Masanz, James J. wrote:
> I'd rather something else than "dictionary-lookup-fast". If we come up with 
> something even faster than this one, having an older one called "fast" could 
> be confusing.
>
> -Original Message-
> From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu] 
> Sent: Monday, June 16, 2014 9:55 AM
> To: cTAKES Developer list
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>
> +1
>
> Dima
>
>
>
>
> On Jun 16, 2014, at 9:42, Miller, Timothy 
>  wrote:
>
>> Sorry to weigh in so late on this -- just returned from vacation. If we
>> want to have a one release delay before making dictionary2 default for
>> testing/documentation/configuration purposes, and there isn't an obvious
>> function-related name, and the main difference is speed, maybe we could
>> call it dictionary-lookup-fast? Besides being accurate and more
>> descriptive than "2", it might lure people into trying it and give us
>> some feedback.
>>
>> Tim
>>
>>
>> On 06/16/2014 10:34 AM, Chen, Pei wrote:
>>> I'm making some significant updates to trunk that may cause some 
>>> instability for this release.
>>> It should be mostly transparent, but let me know if you encounter any 
>>> issues with trunk.
>>>
>>> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
>>> we can leave default to as-is (old behavior).  Folks who wish to give the 
>>> new one a try are welcome to do so and we can change the default behavior 
>>> in a future release.
>>>
>>> [ducks for cover now]
>>> --Pei
>>>
>>>> -Original Message-
>>>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
>>>> Sarma
>>>> Sent: Wednesday, June 11, 2014 9:58 AM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>>>
>>>> Agreed
>>>>
>>>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>>>
>>>>> 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.fi...@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.a...@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?
>>>>>>
>>>>

RE: Preparing for an Apache cTAKES 3.2 Release?

[Masanz, James J.]

I'd rather something else than "dictionary-lookup-fast". If we come up with 
something even faster than this one, having an older one called "fast" could be 
confusing.

-Original Message-
From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu] 
Sent: Monday, June 16, 2014 9:55 AM
To: cTAKES Developer list
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

+1

Dima




On Jun 16, 2014, at 9:42, Miller, Timothy 
 wrote:

> Sorry to weigh in so late on this -- just returned from vacation. If we
> want to have a one release delay before making dictionary2 default for
> testing/documentation/configuration purposes, and there isn't an obvious
> function-related name, and the main difference is speed, maybe we could
> call it dictionary-lookup-fast? Besides being accurate and more
> descriptive than "2", it might lure people into trying it and give us
> some feedback.
> 
> Tim
> 
> 
> On 06/16/2014 10:34 AM, Chen, Pei wrote:
>> I'm making some significant updates to trunk that may cause some instability 
>> for this release.
>> It should be mostly transparent, but let me know if you encounter any issues 
>> with trunk.
>> 
>> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
>> we can leave default to as-is (old behavior).  Folks who wish to give the 
>> new one a try are welcome to do so and we can change the default behavior in 
>> a future release.
>> 
>> [ducks for cover now]
>> --Pei
>> 
>>> -Original Message-
>>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
>>> Sarma
>>> Sent: Wednesday, June 11, 2014 9:58 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>> 
>>> Agreed
>>> 
>>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>> 
>>>> 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.fi...@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.a...@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 
>>>>> wrote:
>>>>> 
>>>>>> I don't have an issue with the *-2 name. I also don't have any
>

RE: Preparing for an Apache cTAKES 3.2 Release?

[Masanz, James J.]

As far as which is the default, I'm curious what the implementers of 
dictionary-lookup2 think. If we have something faster that is equally as good, 
and we know one complaint about cTAKES is its speed, then why not have the new 
one be the default?

-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] 
Sent: Monday, June 16, 2014 9:33 AM
To: dev@ctakes.apache.org
Subject: RE: Preparing for an Apache cTAKES 3.2 Release?

I'm making some significant updates to trunk that may cause some instability 
for this release.
It should be mostly transparent, but let me know if you encounter any issues 
with trunk.

Also, regarding the dictionary-lookup2.  If there are no strong objections, we 
can leave default to as-is (old behavior).  Folks who wish to give the new one 
a try are welcome to do so and we can change the default behavior in a future 
release.

[ducks for cover now]
--Pei

> -Original Message-
> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
> Sarma
> Sent: Wednesday, June 11, 2014 9:58 AM
> To: dev@ctakes.apache.org
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> 
> Agreed
> 
> On Wednesday, June 11, 2014, vijay garla  wrote:
> 
> > 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.fi...@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.a...@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 
> > > 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
> > > > 
> > > > 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-

RE: Preparing for an Apache cTAKES 3.2 Release?

[Savova, Guergana]

+1

Guergana

-Original Message-
From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu] 
Sent: Monday, June 16, 2014 10:56 AM
To: cTAKES Developer list
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

+1

Dima




On Jun 16, 2014, at 9:42, Miller, Timothy 
 wrote:

> Sorry to weigh in so late on this -- just returned from vacation. If 
> we want to have a one release delay before making dictionary2 default 
> for testing/documentation/configuration purposes, and there isn't an 
> obvious function-related name, and the main difference is speed, maybe 
> we could call it dictionary-lookup-fast? Besides being accurate and 
> more descriptive than "2", it might lure people into trying it and 
> give us some feedback.
> 
> Tim
> 
> 
> On 06/16/2014 10:34 AM, Chen, Pei wrote:
>> I'm making some significant updates to trunk that may cause some instability 
>> for this release.
>> It should be mostly transparent, but let me know if you encounter any issues 
>> with trunk.
>> 
>> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
>> we can leave default to as-is (old behavior).  Folks who wish to give the 
>> new one a try are welcome to do so and we can change the default behavior in 
>> a future release.
>> 
>> [ducks for cover now]
>> --Pei
>> 
>>> -Original Message-
>>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of 
>>> Karthik Sarma
>>> Sent: Wednesday, June 11, 2014 9:58 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>> 
>>> Agreed
>>> 
>>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>> 
>>>> 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.fi...@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.a...@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 
>>>>> 
>>>>> 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

Re: Preparing for an Apache cTAKES 3.2 Release?

[Dligach, Dmitriy]

+1

Dima




On Jun 16, 2014, at 9:42, Miller, Timothy 
 wrote:

> Sorry to weigh in so late on this -- just returned from vacation. If we
> want to have a one release delay before making dictionary2 default for
> testing/documentation/configuration purposes, and there isn't an obvious
> function-related name, and the main difference is speed, maybe we could
> call it dictionary-lookup-fast? Besides being accurate and more
> descriptive than "2", it might lure people into trying it and give us
> some feedback.
> 
> Tim
> 
> 
> On 06/16/2014 10:34 AM, Chen, Pei wrote:
>> I'm making some significant updates to trunk that may cause some instability 
>> for this release.
>> It should be mostly transparent, but let me know if you encounter any issues 
>> with trunk.
>> 
>> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
>> we can leave default to as-is (old behavior).  Folks who wish to give the 
>> new one a try are welcome to do so and we can change the default behavior in 
>> a future release.
>> 
>> [ducks for cover now]
>> --Pei
>> 
>>> -Original Message-
>>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
>>> Sarma
>>> Sent: Wednesday, June 11, 2014 9:58 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>> 
>>> Agreed
>>> 
>>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>> 
>>>> 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.fi...@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.a...@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 
>>>>> 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.
>>>>>> 
>>>>>&

RE: Preparing for an Apache cTAKES 3.2 Release?

[Chen, Pei]

I'm making some significant updates to trunk that may cause some instability 
for this release.
It should be mostly transparent, but let me know if you encounter any issues 
with trunk.

Also, regarding the dictionary-lookup2.  If there are no strong objections, we 
can leave default to as-is (old behavior).  Folks who wish to give the new one 
a try are welcome to do so and we can change the default behavior in a future 
release.

[ducks for cover now]
--Pei

> -Original Message-
> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
> Sarma
> Sent: Wednesday, June 11, 2014 9:58 AM
> To: dev@ctakes.apache.org
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> 
> Agreed
> 
> On Wednesday, June 11, 2014, vijay garla  wrote:
> 
> > 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.fi...@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.a...@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 
> > > 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
> > > > 
> > > > 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.fi...@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.
> > > > >> <
> 
> 
> 
> --
> 
> 
> 
> 
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation
> to the House of Delegates of the American Medical Association
> ksa...@ksarma.com
> gchat: ksa...@gmail.com
> linkedin: www.linkedin.com/in/ksarma

Re: Preparing for an Apache cTAKES 3.2 Release?

[Miller, Timothy]

Sorry to weigh in so late on this -- just returned from vacation. If we
want to have a one release delay before making dictionary2 default for
testing/documentation/configuration purposes, and there isn't an obvious
function-related name, and the main difference is speed, maybe we could
call it dictionary-lookup-fast? Besides being accurate and more
descriptive than "2", it might lure people into trying it and give us
some feedback.

Tim


On 06/16/2014 10:34 AM, Chen, Pei wrote:
> I'm making some significant updates to trunk that may cause some instability 
> for this release.
> It should be mostly transparent, but let me know if you encounter any issues 
> with trunk.
>
> Also, regarding the dictionary-lookup2.  If there are no strong objections, 
> we can leave default to as-is (old behavior).  Folks who wish to give the new 
> one a try are welcome to do so and we can change the default behavior in a 
> future release.
>
> [ducks for cover now]
> --Pei
>
>> -Original Message-
>> From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik
>> Sarma
>> Sent: Wednesday, June 11, 2014 9:58 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>>
>> Agreed
>>
>> On Wednesday, June 11, 2014, vijay garla  wrote:
>>
>>> 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.fi...@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.a...@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 
>>>> 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
>>>>> 
>>>>> 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 

RE: Preparing for an Apache cTAKES 3.2 Release?

[Finan, Sean]

> 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:vnga...@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.fi...@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.a...@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 
> 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 
> > 
> > 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.fi...@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.
> > >> 
> > >> wrote:
> > >>
> > >>>
> > >>> Will ctakes-dictionary-lookup2 remain the name for the new 

Re: Preparing for an Apache cTAKES 3.2 Release?

[Karthik Sarma]

Agreed

On Wednesday, June 11, 2014, vijay garla  wrote:

> 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.fi...@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.a...@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 
> > 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
> > > 
> > > 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.fi...@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.
> > > >> <



-- 




--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksa...@ksarma.com
gchat: ksa...@gmail.com
linkedin: www.linkedin.com/in/ksarma

Re: Preparing for an Apache cTAKES 3.2 Release?

[vijay garla]

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.fi...@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.a...@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 
> 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
> > 
> > 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.fi...@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.
> > >> 
> > >> 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.c...@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 

RE: Preparing for an Apache cTAKES 3.2 Release?

[Finan, Sean]

>. 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.a...@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  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 
> 
> 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.fi...@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. 
> >> 
> >> 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.c...@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-197Upgrade cTAKES to Java 7
> >>> CTAKES-292Integrate 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
> >>>
> >>&g

Re: Preparing for an Apache cTAKES 3.2 Release?

[andy mcmurry]

"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  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 
> 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.fi...@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. 
> >> 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.c...@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-197Upgrade cTAKES to Java 7
> >>> CTAKES-292Integrate 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.ja...@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:chen...@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 rel

Re: Preparing for an Apache cTAKES 3.2 Release?

[britt fitch]

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  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.fi...@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. 
>> 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.c...@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-197Upgrade cTAKES to Java 7
>>> CTAKES-292Integrate 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.ja...@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:chen...@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-197Upgrade cTAKES to Java 7
>>>> 
>>>> CTAKES-292Integrate YTEX with cTAKES
>>>> 
>>>> CTAKES-82  Add ctakes-temporal module (Time and Event Annotator
>> +
>>>> DocTimeRel Property only?)
>>>> 
>>>> CTAKES-275some of the older junit tests don't have the right
>>>> Project name in the run configurations
>>>> 
>>>> CTAKES-268Fix SentenceDetector training with updated OpenNLP API
>>>> 
>>>> CTAKES-162Command line scripts leave the user back one directory
>>&

RE: Preparing for an Apache cTAKES 3.2 Release?

[Chen, Pei]

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.fi...@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. 
> 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.c...@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-197Upgrade cTAKES to Java 7
> > CTAKES-292Integrate 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.ja...@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:chen...@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-197Upgrade cTAKES to Java 7
> >>
> >> CTAKES-292Integrate YTEX with cTAKES
> >>
> >> CTAKES-82  Add ctakes-temporal module (Time and Event Annotator
> +
> >> DocTimeRel Property only?)
> >>
> >> CTAKES-275some of the older junit tests don't have the right
> >> Project name in the run configurations
> >>
> >> CTAKES-268Fix SentenceDetector training with updated OpenNLP API
> >>
> >> CTAKES-162Command line scripts leave the user back one directory
> >>
> >> CTAKES-241NullPointerException in ctakes-assertion
> >>
> >> CTAKES-288Severity not set for DiseaseDisorderMention
> >>
> >> CTAKES-239Medication Modifiers do not have the offsets populated
> >>
> >> CTAKES-94  refactoring assertion module to use a cleartk-based
> >> analysis engine (and include evaluation)
> >>
> >> CTAKES-232change concept type
> >>
> >> CTAKES-76  get third party dependencies into Maven Central
> >>
> >> CTAKES-138Remove 3rd party jars from our SVN
> >>
> >> CTAKES-74  Tokenizer PennTreeBank breaks with certain apostrophes
> >> in tokens.
> >>
> >> CTAKES-225Common Type System - Add field to save preferredText in
> >> Segment
> >>
> >> CTAKES-222FirstTokenPermLookupInitializerImpl to suppot arraylist
> >> of DictionaryLookupWindows
> >>
> >> CTAKES-213ModifierExtractorAnnotator 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

Re: Preparing for an Apache cTAKES 3.2 Release?

[britt fitch]

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.  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.c...@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-197Upgrade cTAKES to Java 7
> CTAKES-292Integrate 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.ja...@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:chen...@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-197Upgrade cTAKES to Java 7
>> 
>> CTAKES-292Integrate YTEX with cTAKES
>> 
>> CTAKES-82  Add ctakes-temporal module (Time and Event Annotator +
>> DocTimeRel Property only?)
>> 
>> CTAKES-275some of the older junit tests don't have the right
>> Project name in the run configurations
>> 
>> CTAKES-268Fix SentenceDetector training with updated OpenNLP API
>> 
>> CTAKES-162Command line scripts leave the user back one directory
>> 
>> CTAKES-241NullPointerException in ctakes-assertion
>> 
>> CTAKES-288Severity not set for DiseaseDisorderMention
>> 
>> CTAKES-239Medication Modifiers do not have the offsets populated
>> 
>> CTAKES-94  refactoring assertion module to use a cleartk-based
>> analysis engine (and include evaluation)
>> 
>> CTAKES-232change concept type
>> 
>> CTAKES-76  get third party dependencies into Maven Central
>> 
>> CTAKES-138Remove 3rd party jars from our SVN
>> 
>> CTAKES-74  Tokenizer PennTreeBank breaks with certain apostrophes
>> in tokens.
>> 
>> CTAKES-225Common Type System - Add field to save preferredText in
>> Segment
>> 
>> CTAKES-222FirstTokenPermLookupInitializerImpl to suppot arraylist
>> of DictionaryLookupWindows
>> 
>> CTAKES-213ModifierExtractorAnnotator 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

RE: Preparing for an Apache cTAKES 3.2 Release?

[Chen, Pei]

I'm not sure if it's worth it to keep both for a prolonged period of time. 
We can just replace the old module after the following release?

What are folks preferences? 
I think we can just leave both temporarily for a short transition period (1 
release?). 
--Pei

> -Original Message-
> From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
> Sent: Monday, June 09, 2014 5:18 PM
> To: 'dev@ctakes.apache.org'
> Subject: RE: Preparing for an Apache cTAKES 3.2 Release?
> 
> 
> 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.c...@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-197Upgrade cTAKES to Java 7
> CTAKES-292Integrate 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.ja...@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:chen...@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-197Upgrade cTAKES to Java 7
> >
> > CTAKES-292Integrate YTEX with cTAKES
> >
> > CTAKES-82  Add ctakes-temporal module (Time and Event Annotator +
> > DocTimeRel Property only?)
> >
> > CTAKES-275some of the older junit tests don't have the right
> > Project name in the run configurations
> >
> > CTAKES-268Fix SentenceDetector training with updated OpenNLP API
> >
> > CTAKES-162Command line scripts leave the user back one directory
> >
> > CTAKES-241NullPointerException in ctakes-assertion
> >
> > CTAKES-288Severity not set for DiseaseDisorderMention
> >
> > CTAKES-239Medication Modifiers do not have the offsets populated
> >
> > CTAKES-94  refactoring assertion module to use a cleartk-based
> > analysis engine (and include evaluation)
> >
> > CTAKES-232change concept type
> >
> > CTAKES-76  get third party dependencies into Maven Central
> >
> > CTAKES-138Remove 3rd party jars from our SVN
> >
> > CTAKES-74  Tokenizer PennTreeBank breaks with certain apostrophes
> > in tokens.
> >
> > CTAKES-225Common Type System - Add field to save preferredText in
> > Segment
> >
> > CTAKES-222FirstTokenPermLookupInitializerImpl to suppot arraylist
> > of DictionaryLookupWindows
> >
> > CTAKES-213ModifierExtractorAnnotator 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

RE: Preparing for an Apache cTAKES 3.2 Release?

[Masanz, James J.]

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.c...@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-197Upgrade cTAKES to Java 7
CTAKES-292Integrate 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.ja...@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:chen...@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-197Upgrade cTAKES to Java 7
> 
> CTAKES-292Integrate YTEX with cTAKES
> 
> CTAKES-82  Add ctakes-temporal module (Time and Event Annotator +
> DocTimeRel Property only?)
> 
> CTAKES-275some of the older junit tests don't have the right
> Project name in the run configurations
> 
> CTAKES-268Fix SentenceDetector training with updated OpenNLP API
> 
> CTAKES-162Command line scripts leave the user back one directory
> 
> CTAKES-241NullPointerException in ctakes-assertion
> 
> CTAKES-288Severity not set for DiseaseDisorderMention
> 
> CTAKES-239Medication Modifiers do not have the offsets populated
> 
> CTAKES-94  refactoring assertion module to use a cleartk-based
> analysis engine (and include evaluation)
> 
> CTAKES-232change concept type
> 
> CTAKES-76  get third party dependencies into Maven Central
> 
> CTAKES-138Remove 3rd party jars from our SVN
> 
> CTAKES-74  Tokenizer PennTreeBank breaks with certain apostrophes
> in tokens.
> 
> CTAKES-225Common Type System - Add field to save preferredText in
> Segment
> 
> CTAKES-222FirstTokenPermLookupInitializerImpl to suppot arraylist
> of DictionaryLookupWindows
> 
> CTAKES-213ModifierExtractorAnnotator 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