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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: markable types
Date Thu, 15 May 2014 11:33:47 GMT
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.


From: Anirban Chakraborti [chakraborti.anirban@googlemail.com]
Sent: Sunday, May 11, 2014 9:15 AM
To: dev@ctakes.apache.org
Subject: Re: markable types


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.


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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