Connecting the local UMLS DB to run clinical pipelines

[Bharat Shetty <bh...@gmail.com>]

Can anyone please help me on proper file/location to enter the MySQL
credentials for connecting the local UMLS DB (MySQL) to run advanced
ctakes NLP pipelines that make use of UML data.

In nutshell, any documentation or guidance on connecting to the local
MySQL server that houses the UML data, so that the ctakes clinical
pipelines which are run using runctakesCVD.sh will be able to connect to
the local mysql DB will be most useful.

Regards,
- Bharat

RE: Connecting the local UMLS DB to run clinical pipelines

[Gandhi Rajan Natarajan <Ga...@arisglobal.com>]

Hi Bharat,

I’m not sure whether it’s the ideal way to connect to local MySQL DB for running cTAKES CVD. But this is what I did to make it work:

I updated ‘UmlsLookupAnnotator.xml’ in ‘apache-ctakes-4.0.0\desc\ctakes-dictionary-lookup-fast\desc\analysis_engine’ folder to point to ‘customDictionary.xml’ instead of ‘sno_rx_16ab.xml’

‘customDictionary.xml’ is the file which I generated by using cTAKES dictionary creator GUI. This XML file contains the details of MySQL DB. You can have a look at the XML under https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml

Then you can load ‘AggregatePlaintextFastUMLSProcessor.xml’ under ‘apache-ctakes-4.0.0\desc\ctakes-clinical-pipeline\desc\analysis_engine’ folder for analysis.

I also found ‘DictionaryLookupAnnotatorDB.xml’ under ‘apache-ctakes-4.0.0\desc\ctakes-dictionary-lookup\desc\analysis_engine’ folder which can be used to load dictionary from local DB but I could not able to make it work as I don’t have much expertise in defining custom metadata in ‘LookupDesc_Db.xml’

Regards,
Gandhi

From: Bharat Shetty <bh...@gmail.com>
Sent: Sunday, November 11, 2018 8:01 PM
To: user@ctakes.apache.org
Subject: Connecting the local UMLS DB to run clinical pipelines

Can anyone please help me on proper file/location to enter the MySQL credentials for connecting the local UMLS DB (MySQL) to run advanced ctakes NLP pipelines that make use of UML data.

In nutshell, any documentation or guidance on connecting to the local MySQL server that houses the UML data, so that the ctakes clinical pipelines which are run using runctakesCVD.sh will be able to connect to the local mysql DB will be most useful.

Regards,
- Bharat
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Re: Connecting the local UMLS DB to run clinical pipelines

[Bharat Shetty <bh...@gmail.com>]

Also, when trying out the instructions in the
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation to
install YTEX support to CTakes, I ran into errors shown below for this step:

`../../ant -f build-setup.xml
<https://cwiki.apache.org/confluence/display/CTAKES/build-setup.xml> all`

Could someone tell me how to fix these errors?

Error log is attached. Please suggest what has to be done.

Regards,
Bharat

On Sun, Nov 11, 2018 at 8:00 PM Bharat Shetty <bh...@gmail.com>
wrote:

> Can anyone please help me on proper file/location to enter the MySQL
> credentials for connecting the local UMLS DB (MySQL) to run advanced
> ctakes NLP pipelines that make use of UML data.
>
> In nutshell, any documentation or guidance on connecting to the local
> MySQL server that houses the UML data, so that the ctakes clinical
> pipelines which are run using runctakesCVD.sh will be able to connect to
> the local mysql DB will be most useful.
>
> Regards,
> - Bharat
>