what do they do? lookup window & overlap annotators

["Coarr, Matt" <mc...@mitre.org>]

Does anyone have a quick description of what the lookup window annotator and the overlap annotator do?

I've been looking at the descriptor for LookupWindowAnnotator.xml and its two subcomponents (which use classes OverlapAnnotator and CopyAnnotator).

I'm trying to get a better grasp for what they do.

Thanks!
Matt

Re: what do they do? lookup window & overlap annotators

["Coarr, Matt" <mc...@mitre.org>]

Thanks Britt and James! That's very helpful!

Matt


On 2012-11-14 17:42 , "Masanz, James J." <Ma...@mayo.edu> wrote:

>
>This is all from memory:
>
>In the default pipeline Noun phrases are turned into lookupWindows.
>
>The LookupDesc*.xml file being used describes what type annotation is
>used for a lookup window.
>Sentence is (or at least was at one time) too big to be reasonable both
>for performance purposes and because it would cause words from unrelated
>parts of a sentence to be considered together too often.
>
>LookupWindow annotations were designed to be the input to the dictionary
>lookup component.
>The default pipeline creates LookupWindow annotations from noun phrases
>(including NP PP NP patterns) so that the verb phrases etc are not
>searched.
>
>I believe that the overlap annotator is used in order to keep things
>modular and not be dependent on previous components - to not assume
>LookupWindows are non-overlapping. Overlapping ones get merged into a
>single LookupWindow so that when iterating through all LookupWindow
>annotations, cTAKES won't create multiple annotations for the same
>mention.
>
>-- James
>
>
>> -----Original Message-----
>> From: ctakes-dev-return-847-Masanz.James=mayo.edu@incubator.apache.org
>> [mailto:ctakes-dev-return-847-
>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Coarr, Matt
>> Sent: Wednesday, November 14, 2012 4:20 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: what do they do? lookup window & overlap annotators
>> 
>> Does anyone have a quick description of what the lookup window annotator
>> and the overlap annotator do?
>> 
>> I've been looking at the descriptor for LookupWindowAnnotator.xml and
>> its two subcomponents (which use classes OverlapAnnotator and
>> CopyAnnotator).
>> 
>> I'm trying to get a better grasp for what they do.
>> 
>> Thanks!
>> Matt

RE: what do they do? lookup window & overlap annotators

["Masanz, James J." <Ma...@mayo.edu>]

This is all from memory:

In the default pipeline Noun phrases are turned into lookupWindows.

The LookupDesc*.xml file being used describes what type annotation is used for a lookup window. 
Sentence is (or at least was at one time) too big to be reasonable both for performance purposes and because it would cause words from unrelated parts of a sentence to be considered together too often.

LookupWindow annotations were designed to be the input to the dictionary lookup component.
The default pipeline creates LookupWindow annotations from noun phrases (including NP PP NP patterns) so that the verb phrases etc are not searched.

I believe that the overlap annotator is used in order to keep things modular and not be dependent on previous components - to not assume LookupWindows are non-overlapping. Overlapping ones get merged into a single LookupWindow so that when iterating through all LookupWindow annotations, cTAKES won't create multiple annotations for the same mention.

-- James


> -----Original Message-----
> From: ctakes-dev-return-847-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-847-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Coarr, Matt
> Sent: Wednesday, November 14, 2012 4:20 PM
> To: ctakes-dev@incubator.apache.org
> Subject: what do they do? lookup window & overlap annotators
> 
> Does anyone have a quick description of what the lookup window annotator
> and the overlap annotator do?
> 
> I've been looking at the descriptor for LookupWindowAnnotator.xml and
> its two subcomponents (which use classes OverlapAnnotator and
> CopyAnnotator).
> 
> I'm trying to get a better grasp for what they do.
> 
> Thanks!
> Matt

Re: what do they do? lookup window & overlap annotators

[Britt Fitch <br...@gmail.com>]

Its been a little while since I looked at that but I think this is
used for identifying overlapping concepts within a certain number of
tokens (window) for example:
insulin dependent diabetes mellitus
insulin dependent
diabetes mellitus
etc...

Hopefully my recollection is correct and I am not leading you astray.


On Wed, Nov 14, 2012 at 5:19 PM, Coarr, Matt <mc...@mitre.org> wrote:
> Does anyone have a quick description of what the lookup window annotator and the overlap annotator do?
>
> I've been looking at the descriptor for LookupWindowAnnotator.xml and its two subcomponents (which use classes OverlapAnnotator and CopyAnnotator).
>
> I'm trying to get a better grasp for what they do.
>
> Thanks!
> Matt