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Posted to dev@ctakes.apache.org by Shady Hussein <sh...@gmail.com> on 2013/02/07 11:33:10 UTC
Concepts arenot detected
Hi,
Some concepts are not detected by cTAKES. I want to understand if the
problem is in the UMLS dictionary or it is something else. In my opinion
they are very basic things.
Consider the following example
VITAL SIGNS :
Temperature 97.5 , heart rate 90 , blood pressure 104/80 , respiratory rate
18 .
Here Temperature, blood pressure and respiratory rate arenot annotated as
Concept. Is there a way to annotate them or enhance the dictionary lookup ?
--
Thanks and best Regards,
Shady AbdelAziz
RE: Concepts arenot detected
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
I agree with Tim -- it could be that the concepts in your example are not of the semantic types cTAKES is configured to discover. Of course, you can add more semantic types.
Try this example: "Patient diagnosed with adenocarcinoma." Adenocarcinoma should be discovered.
--Guergana
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Thursday, February 07, 2013 8:01 AM
To: <ct...@incubator.apache.org>
Subject: Re: Concepts arenot detected
Shady,
It may have something to do with the configuration files for the dictionary lookup. There are a lot of things in the UMLS that cTAKES filters out by UMLS Type. If you look in the dictionary project, the LookupDesc_Db.xml has a section of properties for the UMLS consumer, and there is a set of types that are included for each semantic group. For example, the "procedure" group has a property "proceduretuis" that includes the types T059, T060, T061. Looking in the UMLS browser, I couldn't find a TUI for "temperature" that the filter will allow. You can experiment with those types to get more permissive concept labeling. You can explore the semantic types using the Semantic Network Browser in the UMLS Terminology services.
Tim
On Feb 7, 2013, at 5:33 AM, Shady Hussein wrote:
> Hi,
> Some concepts are not detected by cTAKES. I want to understand if the
> problem is in the UMLS dictionary or it is something else. In my
> opinion they are very basic things.
>
> Consider the following example
>
> VITAL SIGNS :
> Temperature 97.5 , heart rate 90 , blood pressure 104/80 , respiratory
> rate
> 18 .
>
> Here Temperature, blood pressure and respiratory rate arenot annotated
> as Concept. Is there a way to annotate them or enhance the dictionary lookup ?
>
> --
> Thanks and best Regards,
>
> Shady AbdelAziz
Re: Concepts arenot detected
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Shady,
It may have something to do with the configuration files for the dictionary lookup. There are a lot of things in the UMLS that cTAKES filters out by UMLS Type. If you look in the dictionary project, the LookupDesc_Db.xml has a section of properties for the UMLS consumer, and there is a set of types that are included for each semantic group. For example, the "procedure" group has a property "proceduretuis" that includes the types T059, T060, T061. Looking in the UMLS browser, I couldn't find a TUI for "temperature" that the filter will allow. You can experiment with those types to get more permissive concept labeling. You can explore the semantic types using the Semantic Network Browser in the UMLS Terminology services.
Tim
On Feb 7, 2013, at 5:33 AM, Shady Hussein wrote:
> Hi,
> Some concepts are not detected by cTAKES. I want to understand if the
> problem is in the UMLS dictionary or it is something else. In my opinion
> they are very basic things.
>
> Consider the following example
>
> VITAL SIGNS :
> Temperature 97.5 , heart rate 90 , blood pressure 104/80 , respiratory rate
> 18 .
>
> Here Temperature, blood pressure and respiratory rate arenot annotated as
> Concept. Is there a way to annotate them or enhance the dictionary lookup ?
>
> --
> Thanks and best Regards,
>
> Shady AbdelAziz
Re: Concepts arenot detected
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Shady,
Could you also provide the full qualified classname of the Concept object? The dictionary lookup annotator normally populates IdentifiedAnnotation.ontologyConceptArr[].UmlsConcept
Just making sure its not a medfacts Concept which is used internally by the assertion module.
Sent from my iPhone
On Feb 7, 2013, at 5:33 AM, "Shady Hussein" <sh...@gmail.com> wrote:
> Hi,
> Some concepts are not detected by cTAKES. I want to understand if the
> problem is in the UMLS dictionary or it is something else. In my opinion
> they are very basic things.
>
> Consider the following example
>
> VITAL SIGNS :
> Temperature 97.5 , heart rate 90 , blood pressure 104/80 , respiratory rate
> 18 .
>
> Here Temperature, blood pressure and respiratory rate arenot annotated as
> Concept. Is there a way to annotate them or enhance the dictionary lookup ?
>
> --
> Thanks and best Regards,
>
> Shady AbdelAziz