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Date: Sat, 17 May 2014 23:03:31 +0530
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Subject: Re: markable types
From: Anirban Chakraborti <chakraborti.anirban@googlemail.com>
To: dev@ctakes.apache.org
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Thanks Timothy,

I get the point but would be greatly helpful if you have an illustrative
example of a tree structure describing the branches and the nodes generated
by Ctakes. I have got an hang how to parse the tree now.


On Thu, May 15, 2014 at 5:03 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> Anir -- I'm not sure I understand your question but from your example it
> doesn't sound like a tree exactly. If you just want a list of medication
> concepts you can do something like:
>
> List<MedicationMention> meds = new ArrayList<>(JCasUtil.select(jcas,
> MedicationMention.class));
> (I believe MedicationMention is the correct class but check your output.)
>
> If you really do want to put them into a syntax tree, there are also
> methods for doing that in AnnotationTreeUtils class.
>
> getAnnotationTree(JCas, Annotation) will give you the tree for the whole
> sentence containing the annotation you give it
> annotationNode(JCas, Annotation) will give you the smallest subtree tree
> covering the annotation you give it.
> insertAnnotationNode(JCas, TopTreebankNode, Annotation, String) will
> insert a node into the tree specified at the level specified by the
> annotation with the category specified by the string. So for example if you
> had meds as above you could then do:
>
> for(MedicationMention med : meds){
>   AnnotationTreeUtils.insertAnnotationNode(jcas,
> AnnotationTreeUtils.getAnnotationTree(jcas, med), med, "MEDICATION")
> }
>
> which would insert a new node into every tree with the label "MEDICATION"
> in every position where a medication was found.
>
> One caveat to the above code is that these methods actually will change
> the tree in the cas. That might be ok for some use cases but for many you
> want to work on a tree outside the cas so that's why there is also methods:
> getTreeCopy(JCas, TopTreebankNode)
> getTreeCopy(JCas, TreebankNode)
>
> if you use the getAnnotationTree method to obtain the tree you want, then
> you can get a copy from these methods, then use the insert methods and do
> something with them immediately (like print them out), without altering the
> originals in the cas if other AEs may use them.
>
> Tim
>
>
>
> ________________________________________
> From: Anirban Chakraborti [chakraborti.anirban@googlemail.com]
> Sent: Sunday, May 11, 2014 9:15 AM
> To: dev@ctakes.apache.org
> Subject: Re: markable types
>
> Steven,
>
> Would you have any example code of tree parser so the output can be
> arranged as per need. I mean, after successful annotation, I want to
> extract certain concepts like medication only and arrange them in a new
> tree so that all annotation in reference to medication concept and their
> sources are listed together.
>
> Anir
>
>
> On Sun, May 11, 2014 at 3:55 PM, Steven Bethard <steven.bethard@gmail.com
> >wrote:
>
> > I don't think "not something anyone would want extracted" should be an
> > argument against anything. We already have constituent and dependency
> > parse trees in the type system, and those would fall under that
> > category.
> >
> > So +1 on markables in the type system. (In general, +1 on moving
> > module-specific types to the standard type system. I'm not sure what
> > the real benefit of splitting them out is...)
> >
> > Steve
> >
> > On Fri, May 9, 2014 at 11:53 AM, Miller, Timothy
> > <Timothy.Miller@childrens.harvard.edu> wrote:
> > > What do people think about taking the "markable" types out of the
> > > coreference project and adding them to the standard type system? This
> is
> > > a pretty standard concept in coreference that doesn't really have a
> > > great natural representation in the current type system -- it
> > > encompasses IdentifiedAnnotations as well as pronouns ("It", "him",
> > > "her") and some determiners ("this").
> > >
> > > The drawback I can see is that it is probably not something anyone
> would
> > > want extracted -- ultimately you want the actual coref pairs or chains.
> > > But it is useful for things like representing gold standard input or
> > > splitting coreference resolution into separate markable recognition and
> > > relation classification steps.
> > >
> > > Tim
> > >
> >
>

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