Thanks Sean. I didn't know about that annotator.
On Fri, Jul 24, 2020, 3:51 AM Finan, Sean <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Sreejith,
>
> Without seeing an example of text I can't say whether my next words will
> help you or not.
>
> If you are using trunk then you should have access to two 'new' annotation
> engines in ctakes-core.
> ListAnnotator - Annotates formatted List Sections by detecting them
> using Regular Expressions provided in an input File.
> ListEntryNegator - Checks List Entries for negation, which may be
> exhibited differently from unstructured negation.
>
> ListAnnotator can use any list of regular expressions in a file. The
> default file is in ctakes-core-res, called DefaultListRegex.bsv
> The format for each line in the regex list is
> NAME||LIST_REGEX||ENTRY_SEPARATOR_REGEX where
> NAME - name of list type. Can be anything.
> LIST_REGEX - some regular expression for which a block of text will
> match a list in its entirety.
> ENTRY_SEPARATOR_REGEX - some regular expression for which text within
> the entire list will match a single list entry.
> For instance, the List
> Smoker Status: N
> Drinking Status: Y
> Pregnant: N/A
> A -simple- line in the regex file could be
> Colonized
> List||(?:^(?:[^\r\n:]+:[^\r\n:]+)+\r?\n){2,}||(?:^(?:[^\r\n:]+:[^\r\n:]+)+\r?\n)
> Notice that each item is separated by two bar characters "||".
>
> The file of regular expressions can be changed using the LIST_TYPES_PATH
> parameter.
>
> ListEntryNegator will iterate through each ListEntry in the cas and use a
> regular expression to determine whether or not items in the list should be
> negated.
> Right now that regex is hard-coded in the class. There should probably be
> a mechanism to overwrite it. ": N" is not in there. Also, only
> Disease/Disorders and Sign/Symptom mentions in the ListEntry are negated.
> You would need to add SmokingStatusAnnotation as a negatable.
>
> I don't know if any of this is helpful, but I thought that I would throw
> it out there.
>
> Sean
> ________________________________________
> From: Sreejith Pk <sreji...@gmail.com>
> Sent: Friday, July 24, 2020 4:09 AM
> To: dev@ctakes.apache.org
> Subject: Re: Clarification regarding NegationFSM [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hi Peter, Thanks a lot for the reply.
>
> Let me elaborate more on the changes I have done so far. I have added
> KuRuleBasedClassifierAnnotator to the pipeline inorder to fetch Smoking
> related keywords from the document. I have
> modified KuRuleBasedClassifierAnnotator in such a way that it will iterate
> through the identified tokens and if the token matches any smoking related
> word which are configured inside a keyword.txt file. The identified tokens
> will be then set to SmokerNamedEntityAnnotation and thus can be read from
> the output XMI.
> Here in my scenario, the sentence I am passing to cTAKES is "Smoking
> status: N". As Smoking is configured inside keywords.txt, it will be coming
> as the output node in SmokerNamedEntityAnnotation. Its polarity only I am
> parsing in my parser logic. Here polarity of SmokerNamedEntityAnnotation
> - "Smoking" token is coming as 1 instead of expected -1
> (NB: I have removed ":" from the NamedEntityContextAnalizer.java - boundary
> words set)
>
> Thanks and Regards,
> Sreejith
>
>
> On Thu, Jul 23, 2020 at 11:20 PM Peter Abramowitsch <
> pabramowit...@gmail.com>
> wrote:
>
> > Check and see if the identified annotation you get for "Smoking status:
> N"
> > without your change is actually "Non Smoker" with polarity 1.
> > Nonsmoker is a separate concept, from a Smoker with polarity -1. Instead
> > of looking at range text, check the canonical text for the concept you
> > have.
> > Having said that, there are many issues with negation in all of the
> > negation annotators. Some are too eager, others are too cautious.
> >
> > Peter
> >
> > On Thu, Jul 23, 2020 at 10:17 AM Sreejith Pk <sreji...@gmail.com> wrote:
> >
> > > Hi Team,
> > >
> > > We are using cTAKES 4.0.0 as the NLP engine in our application. I have
> > > added ContextAnnotator to the pipeline to achieve correct Polarity to
> the
> > > tokens.
> > > After analysing the ContextAnnotator code, I understand that negation
> > > determining condition is written in NegationFSM class.
> > > In my requirement, I have a sentence "Smoking status: N" and I want to
> > set
> > > polarity -1 to the token "Smoking" because of the occurrence of "N". To
> > > achieve the same, I have tried adding "N" to the existing HashSet
> > > in NegationFSM constructor like iv_negVerbsSet.add("N"); But it seems,
> > > polarity of the word token "Smoking" is still coming as 1.
> > > With the same configuration set if I pass "Smoking status: denies", I
> am
> > > getting the polarity of token "Smoking" as -1. Kindly help.
> > >
> > > Thanks & Regards
> > > Sreejith
> > >
> >
>
