RE: Negex
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 wrote: >> Adding triggers requires modifying a text file - much simpler than changing >> code and compiling. > +1 > Thanks Vijay! > -Original Message- > From: vijay garla [mailto:vnga...@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.fi...@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.gr...@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 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
> Adding triggers requires modifying a text file - much simpler than changing > code and compiling. +1 Thanks Vijay! -Original Message- From: vijay garla [mailto:vnga...@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.fi...@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.gr...@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 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
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.fi...@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.gr...@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 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
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.gr...@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 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
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 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
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.gr...@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
