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 [[email protected]]
Sent: Sunday, May 11, 2014 9:15 AM
To: [email protected]
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 <[email protected]>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
> <[email protected]> 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
> >
>
