Help - cTakes with UMLS and Ytex

[Vivek Venugopal <me...@gmail.com>]

Hi,

At the University of Minnesota, We are trying to set up cTakes with UMLS
and see how we can utilize it for the data mining  purposes.
We did the following so far..

1. Installed cTakes
2. set up UMLS in an Oracle data base as per -
https://www.nlm.nih.gov/research/umls/implementation_resources//scripts/README_Semantic_Network_Oracle.html
3. installed YTEX as per -
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation

However, I am not seeing any dictionary lookup tables being created, even
after configuring ytex.properties.


I am desperately looking for any document related to the set up or
guidance..

Thank you,
Vivek Venugopal.

Re: Help - cTakes with UMLS and Ytex

["Abramowitsch, Peter" <pa...@hearst.com>]

Vivek

Chris and I responded to you about 12 hours ago.



On 6/28/16, 10:17 AM, "Vivek Venugopal" <me...@gmail.com> wrote:

>Hi,
>
>Regarding my query on cTakes and UMLS :
>I haven't got any response. Any info would be helpful.
>
>
>Thanks,
>Vivek Venugopal.
>

Re: Help - cTakes with UMLS and Ytex

[Vivek Venugopal <me...@gmail.com>]

Hi,

Regarding my query on cTakes and UMLS :
I haven't got any response. Any info would be helpful.


Thanks,
Vivek Venugopal.

On Mon, Jun 27, 2016 at 1:30 PM, Vivek Venugopal <me...@gmail.com> wrote:

> Hi,
>
> At the University of Minnesota, We are trying to set up cTakes with UMLS
> and see how we can utilize it for the data mining  purposes.
> We did the following so far..
>
> 1. Installed cTakes
> 2. set up UMLS in an Oracle data base as per -
> https://www.nlm.nih.gov/research/umls/implementation_resources//scripts/README_Semantic_Network_Oracle.html
> 3. installed YTEX as per -
> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
>
> However, I am not seeing any dictionary lookup tables being created, even
> after configuring ytex.properties.
>
>
> I am desperately looking for any document related to the set up or
> guidance..
>
> Thank you,
> Vivek Venugopal.
>
>
>
>

Re: Help - cTakes with UMLS and Ytex

["Abramowitsch, Peter" <pa...@hearst.com>]

I'm not sure of Ytex adds another requirement, but is there any reason you
can't just download the pre-built UMLS tables and use the internal Ctakes
hsql DB mechanism as documented here? :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Dictionaries+
and+Models.  

I would also choose the 'Fast UMLS analysis engine' as the original UMLS
engine is far too slow for parsing more than a couple of words at a time.
You can see why it is so slow when stepping through the classical UMLS
engine with a debugger.    The fast AE lookup mechanism, however, is
brilliant!

You won't need Oracle at all for this.

Peter

On 6/27/16, 11:30 AM, "Vivek Venugopal" <me...@gmail.com> wrote:

>Hi,
>
>At the University of Minnesota, We are trying to set up cTakes with UMLS
>and see how we can utilize it for the data mining  purposes.
>We did the following so far..
>
>1. Installed cTakes
>2. set up UMLS in an Oracle data base as per -
>https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_resea
>rch_umls_implementation-5Fresources__scripts_README-5FSemantic-5FNetwork-5
>FOracle.html&d=CwIBaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjw
>uVF4uswNF8BK5Orm10&m=PoYY-jOHdzBE_CLSsyUPISvffwPEkVGO0x88MuY7Qaw&s=ocYET6A
>fFfFTF9WgQn1OchfH8b7BJVA2MeIrE62NzQc&e=
>3. installed YTEX as per -
>https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_conf
>luence_display_CTAKES_YTEX-2BInstallation&d=CwIBaQ&c=B73tqXN8Ec0ocRmZHMCnt
>w&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=PoYY-jOHdzBE_CLSsyUPISvf
>fwPEkVGO0x88MuY7Qaw&s=RMi0Le7JzekqV6yS5hwmMPAlvlGlgW1RMuMoRG-lCgY&e=
>
>However, I am not seeing any dictionary lookup tables being created, even
>after configuring ytex.properties.
>
>
>I am desperately looking for any document related to the set up or
>guidance..
>
>Thank you,
>Vivek Venugopal.