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[protege-discussion] UMLS in Protege but not over the network

Mitch Harris maharri at gmail.com
Fri Feb 8 07:01:58 PST 2008


On Feb 6, 2008 2:03 PM, Tania Tudorache <tudorache at stanford.edu> wrote:
> Mitch Harris wrote:
> > On Feb 5, 2008 8:04 PM, Tania Tudorache <tudorache at stanford.edu> wrote:
> >
> >> I found the place in code where the tab connects to the UMLS RMI server
> >> (at //umlsks.nlm.nih.gov/KSSRetriever). Would it help if I would make
> >> the server name configurable? Of course, this makes sense, only if you
> >> are able to install the server locally.
> >
> > searching the UMLSKS website I find:
> >   http://umlsks.nlm.nih.gov/kss/servlet/Turbine/template/docs%2CDevelGuide%2Cchapter2.vm
> >
> > which basically says that they're working on it but currently you
> > can't run a local KSS server. So the absolute easiest thing (run the
> > server locally, allow one to configure the name of the server for
> > UMLSTab) might be possible eventually, but is not possible right now.
> >
> > The next level would be to bypass the UMLSTab and explicitly link the
> > two statically, that is using the Protege API and UMLS API on the
> > static downloaded UMLSKS files. Unfortunately, that has a higher
> > labor/time/learning curve cost to it.
>
> I think you will be able to reuse almost all the code from the UMLSTab
> that interacts with the KSS-API. If they have a method to load a UMLS
> model from a file in KSS-API, then all you'll have to do is to replace
> the initialization method, which is very easy to do.

After looking at the UMLSTab code, that direction that seems promising
(but not just the init method). I don't want to go to the trouble of
creating a local server version of UMLSKS -and- subclass the
KSSRetriever (the class that makes calls to the UMLSKS server for
'getConceptName' or 'getSemanticType'). What I suspect is easier is to
just implement those functions directly on the downloaded files
(presuming that the UMLS files are not terribly difficult to parse).

Mitch



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