Drugs being filtered out..

[Prasanna Bala <ba...@gmail.com>]

Hi,

I want to run and tag the entities for all the semantic types in the
cTakes. I read the tutorial and found that we can include our semantic
types in the LookupDesc_Db.xml. I added my own property in the
configuration file

<property key="drugTuis" value="">.

Then I run the AggregatePlaintextUMLSProcessor.xml. But I was not able to
detect the drug entities. I am also getting the chemicals getting filtered
out by OrangeBookFilterConsumerImpl. However, I commented out the the in
the xml file. Can someone tell me what should I specifically do to add drug
entities. I also want to use all the 133 TUIs of UMLS for a use case.

Regards,
Prasanna

RE: Drugs being filtered out..

["Savova, Guergana" <Gu...@childrens.harvard.edu>]

A further clarification - cTAKES currently implements 5 of the UMLS semantic groups (semantic group consists of semantic types). If you'd like to use all 133 UMLS semantic types, you'd need to extend cTAKES code to accommodate them.

Hope this helps.
--Guergana

-----Original Message-----
From: britt fitch [mailto:britt.fitch@wiredinformatics.com] 
Sent: Monday, April 21, 2014 8:37 AM
To: user@ctakes.apache.org
Subject: Re: Drugs being filtered out..

Hi Prasanna, 

The value of that property needs to be a comma separated list of TUIs.
Also from a quick look in UmlsToSnomedConsumerImpl which I think is the parent class of what is being used in that xml file the key it is expecting is 'medicationTuis' rather than 'drugTuis'. 

Hope that helps,

Britt


On Apr 21, 2014, at 7:11 AM, Prasanna Bala <ba...@gmail.com> wrote:

> Hi,
> 
> I want to run and tag the entities for all the semantic types in the cTakes. I read the tutorial and found that we can include our semantic types in the LookupDesc_Db.xml. I added my own property in the configuration file 
> 
> <property key="drugTuis" value="">.
> 
> Then I run the AggregatePlaintextUMLSProcessor.xml. But I was not able to detect the drug entities. I am also getting the chemicals getting filtered out by OrangeBookFilterConsumerImpl. However, I commented out the the in the xml file. Can someone tell me what should I specifically do to add drug entities. I also want to use all the 133 TUIs of UMLS for a use case.
> 
> Regards,
> Prasanna

Re: Drugs being filtered out..

[britt fitch <br...@wiredinformatics.com>]

Hi Prasanna, 

The value of that property needs to be a comma separated list of TUIs.
Also from a quick look in UmlsToSnomedConsumerImpl which I think is the parent class of what is being used in that xml file the key it is expecting is ‘medicationTuis’ rather than ‘drugTuis’. 

Hope that helps,

Britt


On Apr 21, 2014, at 7:11 AM, Prasanna Bala <ba...@gmail.com> wrote:

> Hi,
> 
> I want to run and tag the entities for all the semantic types in the cTakes. I read the tutorial and found that we can include our semantic types in the LookupDesc_Db.xml. I added my own property in the configuration file 
> 
> <property key="drugTuis" value="">.
> 
> Then I run the AggregatePlaintextUMLSProcessor.xml. But I was not able to detect the drug entities. I am also getting the chemicals getting filtered out by OrangeBookFilterConsumerImpl. However, I commented out the the in the xml file. Can someone tell me what should I specifically do to add drug entities. I also want to use all the 133 TUIs of UMLS for a use case.
> 
> Regards,
> Prasanna