Re: Textmarker: delete contained annotations

2013-05-01 Thread Peter Klügl 

Hi,

Am 01.05.2013 04:57, schrieb William Karl Thompson:

Hi,

I'm working with the cTAKES pipeline to annotate some clinical text. The cTAKES 
syntactic chunker generates overlapping and nested annotations with the same 
syntactic type. For example:

[NP ascending [NP colon polyps]]

What I would like to do is to use TextMarker rules to eliminate nested 
annotations, so at the end of the day just have the following:

[NP colon ascending polyps]

I've tried to use UNMARK, but the following two rules appear to remove all NPs 
starting at the first match, even the containing annotation:

NP{PARTOF(NP)-UNMARK(NP)};
NP{CONTAINS(NP)-UNMARK(NP)};

Is there way to accomplish this that I'm missing? Using loops perhaps?


The simplest solution in your situation would be:

NP{PARTOFNEQ(NP) - UNMARK(NP)};

(PARTOFNEQ: part of, but not equal)

If it gets more complicated, then something with a loop and/or 
additional types is necessary:


BLOCK(forEach) Test{} {
ANY+? Test{- UNMARK(Test)};
Test{- UNMARK(Test)} ANY;
}


Best,

Peter


Thanks,

Will

RE: Textmarker: delete contained annotations

2013-05-01 Thread William Karl Thompson 
Thanks Peter! I have read the documentation, but forgot about that condition.

From: Peter Klügl [pklu...@uni-wuerzburg.de]
Sent: Wednesday, May 01, 2013 6:18 AM
To: user@uima.apache.org
Subject: Re: Textmarker: delete contained annotations

Hi,

Am 01.05.2013 04:57, schrieb William Karl Thompson:
 Hi,

 I'm working with the cTAKES pipeline to annotate some clinical text. The 
 cTAKES syntactic chunker generates overlapping and nested annotations with 
 the same syntactic type. For example:

 [NP ascending [NP colon polyps]]

 What I would like to do is to use TextMarker rules to eliminate nested 
 annotations, so at the end of the day just have the following:

 [NP colon ascending polyps]

 I've tried to use UNMARK, but the following two rules appear to remove all 
 NPs starting at the first match, even the containing annotation:

 NP{PARTOF(NP)-UNMARK(NP)};
 NP{CONTAINS(NP)-UNMARK(NP)};

 Is there way to accomplish this that I'm missing? Using loops perhaps?

The simplest solution in your situation would be:

NP{PARTOFNEQ(NP) - UNMARK(NP)};

(PARTOFNEQ: part of, but not equal)

If it gets more complicated, then something with a loop and/or
additional types is necessary:

BLOCK(forEach) Test{} {
 ANY+? Test{- UNMARK(Test)};
 Test{- UNMARK(Test)} ANY;
}


Best,

Peter

 Thanks,

 Will