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Posted to dev@ctakes.apache.org by "Green, John" <jo...@usuhs.edu> on 2015/01/05 18:41:49 UTC
Negex
Hi all - Does anyone know off the top of their head if the negex trigger
rules included in the original 2009 python script were added to when it was
implemented in ctakes?
Thanks,
John
RE: Negex
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
Yes, they were added in the rule-based implementation. You can still use it if you'd like.
--Guergana
-----Original Message-----
From: Green, John [mailto:john.green@usuhs.edu]
Sent: Monday, January 05, 2015 12:59 PM
To: dev@ctakes.apache.org
Subject: Negex
Hi all - Does anyone know off the top of their head if the negex trigger rules included in the original 2009 python script were added to when it was implemented in ctakes?
Thanks,
John
RE: Negex
Posted by John Green <jo...@gmail.com>.
Thank you both very much. That was very helpful.
Best,
JG
—
Sent from Mailbox
On Mon, Jan 5, 2015 at 3:17 PM, Finan, Sean
<Se...@childrens.harvard.edu> wrote:
>> Adding triggers requires modifying a text file - much simpler than changing code and compiling.
> +1
> Thanks Vijay!
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Monday, January 05, 2015 3:13 PM
> To: dev@ctakes.apache.org
> Subject: Re: Negex
> I think the original ctakes negation AE is in the spirit of Negex, but it is not Negex. AFAICT the ctakes negation AE
> * requires that triggers are single tokens
> * does not support conjuctions (e.g. however, nevertheless) or post-negation triggers (e.g. free, was ruled out)
> * is based on a FSM, which is different from the way Negex rules work
> * requires modifying and recompiling code to add negation triggers
> We ported the Negex algorithm 1-1 to UIMA to address these issues. See the ctakes-ytex-uima\desc\analysis_engine\NegexAnnotator.xml and the corresponding trigger file
> (ctakes-ytex-res\src\main\resources\org\apache\ctakes\ytex\negex\negex_triggers.txt)
> Adding triggers requires modifying a text file - much simpler than changing code and compiling.
> -vj
> On Mon, Jan 5, 2015 at 8:30 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
>> I don't know. I'm comparing what I think is the 2009 negex trigger
>> set
>> https://code.google.com/p/negex/source/browse/trunk/GeneralNegEx.Java.
>> v.1.2.05092009/negex_triggers.txt
>>
>> with the cTakes trigger set in
>> org.apache.ctakes.core.fsm.machine.NegationFSM.java and it looks like
>> the cTakes set is missing some 2009 negex trigger words, such as "exhibit".
>>
>> Anyway, you can read
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Con
>> texts for info on adding triggers to the cTakes version.
>>
>> Sean
>>
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Monday, January 05, 2015 2:03 PM
>> To: dev@ctakes.apache.org
>> Cc: dev@ctakes.apache.org
>> Subject: Re: Negex
>>
>> Thanks Ma'am for the input!
>>
>>
>> So to clarify: ctakes added additional trigger words to the list
>> published originally? (This is an unrelated question to the negex vs
>> ml thread last month).
>>
>>
>>
>>
>> Best,
>>
>> John
>> —
>> Sent from Mailbox
>>
>> On Mon, Jan 5, 2015 at 12:58 PM, Green, John <jo...@usuhs.edu> wrote:
>>
>> > Hi all - Does anyone know off the top of their head if the negex
>> > trigger rules included in the original 2009 python script were added
>> > to when it was implemented in ctakes?
>> > Thanks,
>> > John
>>
RE: Negex
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
> Adding triggers requires modifying a text file - much simpler than changing code and compiling.
+1
Thanks Vijay!
-----Original Message-----
From: vijay garla [mailto:vngarla@gmail.com]
Sent: Monday, January 05, 2015 3:13 PM
To: dev@ctakes.apache.org
Subject: Re: Negex
I think the original ctakes negation AE is in the spirit of Negex, but it is not Negex. AFAICT the ctakes negation AE
* requires that triggers are single tokens
* does not support conjuctions (e.g. however, nevertheless) or post-negation triggers (e.g. free, was ruled out)
* is based on a FSM, which is different from the way Negex rules work
* requires modifying and recompiling code to add negation triggers
We ported the Negex algorithm 1-1 to UIMA to address these issues. See the ctakes-ytex-uima\desc\analysis_engine\NegexAnnotator.xml and the corresponding trigger file
(ctakes-ytex-res\src\main\resources\org\apache\ctakes\ytex\negex\negex_triggers.txt)
Adding triggers requires modifying a text file - much simpler than changing code and compiling.
-vj
On Mon, Jan 5, 2015 at 8:30 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> I don't know. I'm comparing what I think is the 2009 negex trigger
> set
> https://code.google.com/p/negex/source/browse/trunk/GeneralNegEx.Java.
> v.1.2.05092009/negex_triggers.txt
>
> with the cTakes trigger set in
> org.apache.ctakes.core.fsm.machine.NegationFSM.java and it looks like
> the cTakes set is missing some 2009 negex trigger words, such as "exhibit".
>
> Anyway, you can read
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Con
> texts for info on adding triggers to the cTakes version.
>
> Sean
>
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Monday, January 05, 2015 2:03 PM
> To: dev@ctakes.apache.org
> Cc: dev@ctakes.apache.org
> Subject: Re: Negex
>
> Thanks Ma'am for the input!
>
>
> So to clarify: ctakes added additional trigger words to the list
> published originally? (This is an unrelated question to the negex vs
> ml thread last month).
>
>
>
>
> Best,
>
> John
> —
> Sent from Mailbox
>
> On Mon, Jan 5, 2015 at 12:58 PM, Green, John <jo...@usuhs.edu> wrote:
>
> > Hi all - Does anyone know off the top of their head if the negex
> > trigger rules included in the original 2009 python script were added
> > to when it was implemented in ctakes?
> > Thanks,
> > John
>
Re: Negex
Posted by vijay garla <vn...@gmail.com>.
I think the original ctakes negation AE is in the spirit of Negex, but it
is not Negex. AFAICT the ctakes negation AE
* requires that triggers are single tokens
* does not support conjuctions (e.g. however, nevertheless) or
post-negation triggers (e.g. free, was ruled out)
* is based on a FSM, which is different from the way Negex rules work
* requires modifying and recompiling code to add negation triggers
We ported the Negex algorithm 1-1 to UIMA to address these issues. See the
ctakes-ytex-uima\desc\analysis_engine\NegexAnnotator.xml and the
corresponding trigger file
(ctakes-ytex-res\src\main\resources\org\apache\ctakes\ytex\negex\negex_triggers.txt)
Adding triggers requires modifying a text file - much simpler than changing
code and compiling.
-vj
On Mon, Jan 5, 2015 at 8:30 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> I don't know. I'm comparing what I think is the 2009 negex trigger set
> https://code.google.com/p/negex/source/browse/trunk/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt
>
> with the cTakes trigger set in
> org.apache.ctakes.core.fsm.machine.NegationFSM.java and it looks like the
> cTakes set is missing some 2009 negex trigger words, such as "exhibit".
>
> Anyway, you can read
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
> for info on adding triggers to the cTakes version.
>
> Sean
>
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Monday, January 05, 2015 2:03 PM
> To: dev@ctakes.apache.org
> Cc: dev@ctakes.apache.org
> Subject: Re: Negex
>
> Thanks Ma'am for the input!
>
>
> So to clarify: ctakes added additional trigger words to the list published
> originally? (This is an unrelated question to the negex vs ml thread last
> month).
>
>
>
>
> Best,
>
> John
> —
> Sent from Mailbox
>
> On Mon, Jan 5, 2015 at 12:58 PM, Green, John <jo...@usuhs.edu> wrote:
>
> > Hi all - Does anyone know off the top of their head if the negex
> > trigger rules included in the original 2009 python script were added
> > to when it was implemented in ctakes?
> > Thanks,
> > John
>
RE: Negex
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
I don't know. I'm comparing what I think is the 2009 negex trigger set https://code.google.com/p/negex/source/browse/trunk/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt
with the cTakes trigger set in org.apache.ctakes.core.fsm.machine.NegationFSM.java and it looks like the cTakes set is missing some 2009 negex trigger words, such as "exhibit".
Anyway, you can read https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts for info on adding triggers to the cTakes version.
Sean
-----Original Message-----
From: John Green [mailto:john.travis.green@gmail.com]
Sent: Monday, January 05, 2015 2:03 PM
To: dev@ctakes.apache.org
Cc: dev@ctakes.apache.org
Subject: Re: Negex
Thanks Ma'am for the input!
So to clarify: ctakes added additional trigger words to the list published originally? (This is an unrelated question to the negex vs ml thread last month).
Best,
John
—
Sent from Mailbox
On Mon, Jan 5, 2015 at 12:58 PM, Green, John <jo...@usuhs.edu> wrote:
> Hi all - Does anyone know off the top of their head if the negex
> trigger rules included in the original 2009 python script were added
> to when it was implemented in ctakes?
> Thanks,
> John
Re: Negex
Posted by John Green <jo...@gmail.com>.
Thanks Ma'am for the input!
So to clarify: ctakes added additional trigger words to the list published originally? (This is an unrelated question to the negex vs ml thread last month).
Best,
John
—
Sent from Mailbox
On Mon, Jan 5, 2015 at 12:58 PM, Green, John <jo...@usuhs.edu> wrote:
> Hi all - Does anyone know off the top of their head if the negex trigger
> rules included in the original 2009 python script were added to when it was
> implemented in ctakes?
> Thanks,
> John