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[protege-discussion] FW: UMLS TAB_problems

Jennifer Vendetti vendetti at stanford.edu
Thu Oct 23 16:27:42 PDT 2008


Hello George,

GEORGE LITSIOS wrote:
> I'm trying to make a simple ontology in the domain of cardiovascular 
> diseases, and i'm trying to enrich it with the UMLS_TAB.   I'm at the 
> position making tests with UMLS_TAB so to see how is that working.   I 
> have this problems at that time:
>  
> 1: The approximate matching doesn't work, the program saying to me 
> that: "Approximate matching is unavailable for this release of 
> software" (I'm using protege 3.3)

I was able to reproduce this error message.  This is an error that is 
being generated by the UMLSKS API from the National Library of 
Medicine.  It does not have anything to do with the version of Protege 
you are using.  I will have to look into whether or not we could fix 
this - time permitting.

Also, there are a few things you should do here:

1).  Upgrade to Protege 3.4 beta.  We are getting close to making this 
an official release.

2).  Configure Protege to use a more recent UMLS release number.  The 
default value is old - something like 2004AA.  I will see about getting 
this fixed for the next build.  In the mean time, you can follow 
instructions on the wiki for setting the release number to the most 
current (2008AA):

http://protegewiki.stanford.edu/index.php/UMLS_Tab#UMLS_Releases

>  2: When i'm trying to inport a class with all it's slots in my 
> ontology, it doesn't inport synonyms and anything else exept the 
> definition

I'm not sure that this is documented anywhere, but are you importing 
classes as a subclass of the KB_ROOT class?  You'll notice that KB_ROOT 
is added to your ontology when you configure Protege to show the UMLS 
Tab and the class is already configured with the necessary set of slots 
to pull in data that the UMLS generates, e.g.:



>  
> 3:Is UMLS_TAB working with owl ontologies wich are made with 
> protege?Or only with Protege Project type "Protege FIles (.pont and 
> .pins)" ?

The UMLS Tab was developed quite a number of years ago before the 
Protege-OWL editor existed.  It has not been tested with Protege-OWL.  
If possible, it would be better to develop using Protege-Frames and then 
convert your ontology to OWL via File | Convert Project to Format...

Jennifer

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