Re: rule-based lookup for custom lexicon [EXTERNAL]

2021-05-18 Thread Finan, Sean 
 To which ctakes component(s) are you referring? 

From: Greg Silverman 
Sent: Sunday, May 16, 2021 6:02 PM
To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
Subject: rule-based lookup for custom lexicon [EXTERNAL]

* External Email - Caution *


I looked all over and could not find any information on how to add this
pipeline component to cTAKES. I assume it uses UIMA Ruta?

Thanks in advance!

Greg--
--
Greg M. Silverman
Senior Systems Developer
NLP/IE 

Department of Surgery
University of Minnesota
g...@umn.edu

Re: rule-based lookup for custom lexicon [EXTERNAL]

2021-05-18 Thread Greg Silverman 
Hi Sean,
I was wondering if there was a way to use rule-base lookup of a custom
lexicon within cTAKES (say a locally curated list of covd-19 symptoms).
When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything
wrt to cTAKES specifics.

Thanks!


Greg--

On Tue, May 18, 2021 at 10:04 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

>  To which ctakes component(s) are you referring?
> 
> From: Greg Silverman 
> Sent: Sunday, May 16, 2021 6:02 PM
> To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
> Subject: rule-based lookup for custom lexicon [EXTERNAL]
>
> * External Email - Caution *
>
>
> I looked all over and could not find any information on how to add this
> pipeline component to cTAKES. I assume it uses UIMA Ruta?
>
> Thanks in advance!
>
> Greg--
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE <
> https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!6hN356eDesvWNYzsrDMaXgF6IkZw313QU2QUQw5M8Jysvh1K1JxjEBeztZicX1DM2jC0o7_0qAA$
> >
> Department of Surgery
> University of Minnesota
> g...@umn.edu
>


-- 
Greg M. Silverman
Senior Systems Developer
NLP/IE 
Department of Surgery
University of Minnesota
g...@umn.edu

Re: rule-based lookup for custom lexicon [EXTERNAL]

2021-05-18 Thread Finan, Sean 
Hi Greg,

>From 30,000 ft, I think that you would want to use the RutaEngine.

https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.ae.basic
https://javadoc.io/doc/org.apache.uima/ruta-core/latest/org/apache/uima/ruta/engine/RutaEngine.html
http://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-core/src/main/java/org/apache/uima/ruta/engine/RutaEngine.java

That seems to be the actual analysis engine that loads and uses rules to create 
annotations.
While you could use an xml descriptor or use the piper "set" command and do 
things like mapping ruta to ctakes type systems, I would take the alternate 
approach of "copying" the initialize(..) and process (..) methods and modify 
them to use ctakes types directly.

Disclaimer:  I know very little about uima ruta.  At some point I did look into 
it but it was for a specific (ctakes-derivative) project and I didn't go 
further than basic doc perusal.  

If you move forward with this please let us all know what you find.  I think 
that there will be great interest in the community.

Sean

From: Greg Silverman 
Sent: Tuesday, May 18, 2021 11:13 AM
To: dev@ctakes.apache.org
Cc: Himanshu Shekhar Sahoo
Subject: Re: rule-based lookup for custom lexicon [EXTERNAL]

* External Email - Caution *


Hi Sean,
I was wondering if there was a way to use rule-base lookup of a custom
lexicon within cTAKES (say a locally curated list of covd-19 symptoms).
When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything
wrt to cTAKES specifics.

Thanks!


Greg--

On Tue, May 18, 2021 at 10:04 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

>  To which ctakes component(s) are you referring?
> 
> From: Greg Silverman 
> Sent: Sunday, May 16, 2021 6:02 PM
> To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
> Subject: rule-based lookup for custom lexicon [EXTERNAL]
>
> * External Email - Caution *
>
>
> I looked all over and could not find any information on how to add this
> pipeline component to cTAKES. I assume it uses UIMA Ruta?
>
> Thanks in advance!
>
> Greg--
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE <
> https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!6hN356eDesvWNYzsrDMaXgF6IkZw313QU2QUQw5M8Jysvh1K1JxjEBeztZicX1DM2jC0o7_0qAA$
> >
> Department of Surgery
> University of Minnesota
> g...@umn.edu
>


--
Greg M. Silverman
Senior Systems Developer
NLP/IE 

Department of Surgery
University of Minnesota
g...@umn.edu

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

2021-05-18 Thread Miller, Timothy 
But Sean, isn't what he's asking for essentially already implemented in cTAKES 
as the custom dictionary? I'm currently using that approach for my covid 
container:
https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container
Tim


From: Finan, Sean 
Sent: Tuesday, May 18, 2021 11:55 AM
To: dev@ctakes.apache.org
Cc: Himanshu Shekhar Sahoo
Subject: Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

* External Email - Caution *


Hi Greg,

>From 30,000 ft, I think that you would want to use the RutaEngine.

https://urldefense.com/v3/__https://uima.apache.org/d/ruta-current/tools.ruta.book.html*ugr.tools.ruta.ae.basic__;Iw!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickztninUTU$
https://urldefense.com/v3/__https://javadoc.io/doc/org.apache.uima/ruta-core/latest/org/apache/uima/ruta/engine/RutaEngine.html__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzI7QF5CI$
https://urldefense.com/v3/__http://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-core/src/main/java/org/apache/uima/ruta/engine/RutaEngine.java__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzJJ96zT4$

That seems to be the actual analysis engine that loads and uses rules to create 
annotations.
While you could use an xml descriptor or use the piper "set" command and do 
things like mapping ruta to ctakes type systems, I would take the alternate 
approach of "copying" the initialize(..) and process (..) methods and modify 
them to use ctakes types directly.

Disclaimer:  I know very little about uima ruta.  At some point I did look into 
it but it was for a specific (ctakes-derivative) project and I didn't go 
further than basic doc perusal.

If you move forward with this please let us all know what you find.  I think 
that there will be great interest in the community.

Sean

From: Greg Silverman 
Sent: Tuesday, May 18, 2021 11:13 AM
To: dev@ctakes.apache.org
Cc: Himanshu Shekhar Sahoo
Subject: Re: rule-based lookup for custom lexicon [EXTERNAL]

* External Email - Caution *


Hi Sean,
I was wondering if there was a way to use rule-base lookup of a custom
lexicon within cTAKES (say a locally curated list of covd-19 symptoms).
When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything
wrt to cTAKES specifics.

Thanks!


Greg--

On Tue, May 18, 2021 at 10:04 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

>  To which ctakes component(s) are you referring?
> 
> From: Greg Silverman 
> Sent: Sunday, May 16, 2021 6:02 PM
> To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
> Subject: rule-based lookup for custom lexicon [EXTERNAL]
>
> * External Email - Caution *
>
>
> I looked all over and could not find any information on how to add this
> pipeline component to cTAKES. I assume it uses UIMA Ruta?
>
> Thanks in advance!
>
> Greg--
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE <
> https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!6hN356eDesvWNYzsrDMaXgF6IkZw313QU2QUQw5M8Jysvh1K1JxjEBeztZicX1DM2jC0o7_0qAA$
> >
> Department of Surgery
> University of Minnesota
> g...@umn.edu
>


--
Greg M. Silverman
Senior Systems Developer
NLP/IE 

Department of Surgery
University of Minnesota
g...@umn.edu

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

2021-05-18 Thread Peter Abramowitsch 
Hi All,  yes,  the line between "lookup" and rule execution is a little
blurry sometimes.   Here's some more blurriness.

I've done something related, adapting a UIMA tokens regex engine for
Ctakes.  You create a new type in the TypeSystem.  In my case it uses
CONLLDEP Annotations as the tokens to reason over.   You can set up
expressions (rules) that look like this.
(Yes, this case is already covered in the dictionary, but it's an example)

Matcher A:   (lemma=="be");
Matcher B:   /partially|partly/;
Matcher C:   /vaccinated/;

Rule  vaccinated|CUI1234|SNOMED5678:  A? B?  C;

You get the Annotation you've delegated to this task, with the entity
value  "vaccinated|1234|5678"  and the range which spanned the tokens that
caused the annotation rule to fire

(See Stanford's Tokens Regex)

Peter


On Tue, May 18, 2021 at 1:29 PM Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:

> But Sean, isn't what he's asking for essentially already implemented in
> cTAKES as the custom dictionary? I'm currently using that approach for my
> covid container:
>
> https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container
> Tim
>
> 
> From: Finan, Sean 
> Sent: Tuesday, May 18, 2021 11:55 AM
> To: dev@ctakes.apache.org
> Cc: Himanshu Shekhar Sahoo
> Subject: Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]
>
> * External Email - Caution *
>
>
> Hi Greg,
>
> From 30,000 ft, I think that you would want to use the RutaEngine.
>
>
> https://urldefense.com/v3/__https://uima.apache.org/d/ruta-current/tools.ruta.book.html*ugr.tools.ruta.ae.basic__;Iw!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickztninUTU$
>
> https://urldefense.com/v3/__https://javadoc.io/doc/org.apache.uima/ruta-core/latest/org/apache/uima/ruta/engine/RutaEngine.html__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzI7QF5CI$
>
> https://urldefense.com/v3/__http://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-core/src/main/java/org/apache/uima/ruta/engine/RutaEngine.java__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzJJ96zT4$
>
> That seems to be the actual analysis engine that loads and uses rules to
> create annotations.
> While you could use an xml descriptor or use the piper "set" command and
> do things like mapping ruta to ctakes type systems, I would take the
> alternate approach of "copying" the initialize(..) and process (..) methods
> and modify them to use ctakes types directly.
>
> Disclaimer:  I know very little about uima ruta.  At some point I did look
> into it but it was for a specific (ctakes-derivative) project and I didn't
> go further than basic doc perusal.
>
> If you move forward with this please let us all know what you find.  I
> think that there will be great interest in the community.
>
> Sean
> 
> From: Greg Silverman 
> Sent: Tuesday, May 18, 2021 11:13 AM
> To: dev@ctakes.apache.org
> Cc: Himanshu Shekhar Sahoo
> Subject: Re: rule-based lookup for custom lexicon [EXTERNAL]
>
> * External Email - Caution *
>
>
> Hi Sean,
> I was wondering if there was a way to use rule-base lookup of a custom
> lexicon within cTAKES (say a locally curated list of covd-19 symptoms).
> When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything
> wrt to cTAKES specifics.
>
> Thanks!
>
>
> Greg--
>
> On Tue, May 18, 2021 at 10:04 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> >  To which ctakes component(s) are you referring?
> > 
> > From: Greg Silverman 
> > Sent: Sunday, May 16, 2021 6:02 PM
> > To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
> > Subject: rule-based lookup for custom lexicon [EXTERNAL]
> >
> > * External Email - Caution *
> >
> >
> > I looked all over and could not find any information on how to add this
> > pipeline component to cTAKES. I assume it uses UIMA Ruta?
> >
> > Thanks in advance!
> >
> > Greg--
> > --
> > Greg M. Silverman
> > Senior Systems Developer
> > NLP/IE <
> >
> https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!6hN356eDesvWNYzsrDMaXgF6IkZw313QU2QUQw5M8Jysvh1K1JxjEBeztZicX1DM2jC0o7_0qAA$
> > >
> > Department of Surgery
> > University of Minnesota
> > g...@umn.edu
> >
>
>
> --
> Greg M. Silverman
> Senior Systems Developer
> NLP/IE <
> https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!8uKf_4SXyKdCmvlMHvRGddxlzofg64D4_zsPdCThqeMAyn2akyMNI8wqM6yNUZA2N93F-aAsR7I$
> >
> Department of Surgery
> University of Minnesota
> g...@umn.edu
>