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[protege-discussion] UMLS TAB_problems

GEORGE LITSIOS litsiosgeorgios at hotmail.com
Thu Oct 23 23:44:50 PDT 2008


Thanks Jennifer for your response,
 
So the problem with approximate matching i thing that will not be solve, right?
 
Without change the UMLS version of metathesaurus, the UMLS_TAB not working, i had changed it to 2008AA before sent my questions at the mailing list.
 
Also, for the second question, why not inserting the slots of umls, i found that if i start the project as "frames" then it works. I started the project as "owl/rdf" and for this reason it didn't worked.  I guess there is no way to work with "owl/rdf".
 
Can you tell me if i start the project as "frames", if i will encounter any problem, if i convert it in owl with protege converter?I have in mind to use the .owl file with Jena in the future for indexing documents on owl classes or something like that,and for querying the ontology for retrieving documents. 
 
Can you also explain me the usefulness of "KB_ROOT"?
 
Thanks in advance
George> From: protege-discussion-request at lists.stanford.edu> Subject: protege-discussion Digest, Vol 27, Issue 24> To: protege-discussion at lists.stanford.edu> Date: Thu, 23 Oct 2008 16:27:59 -0700> > Send protege-discussion mailing list submissions to> protege-discussion at lists.stanford.edu> > To subscribe or unsubscribe via the World Wide Web, visit> https://mailman.stanford.edu/mailman/listinfo/protege-discussion> or, via email, send a message with subject or body 'help' to> protege-discussion-request at lists.stanford.edu> > You can reach the person managing the list at> protege-discussion-owner at lists.stanford.edu> > When replying, please edit your Subject line so it is more specific> than "Re: Contents of protege-discussion digest..."> > > Today's Topics:> > 1. Re: WEBSITE PROBLEM REPORT: protegewiki does not show plug-in> versions (Jennifer Vendetti)> 2. Re: FW: UMLS TAB_problems (Jennifer Vendetti)> > > ----------------------------------------------------------------------> > Message: 1> Date: Thu, 23 Oct 2008 14:57:48 -0700> From: Jennifer Vendetti <vendetti at stanford.edu>> Subject: Re: [protege-discussion] WEBSITE PROBLEM REPORT: protegewiki> does not show plug-in versions> To: protege at ontospace.net, protege-discussion> <protege-discussion at mailman.stanford.edu>> Message-ID: <4900F35C.4040106 at stanford.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed> > Hello Len,> > Most of the wiki issues have been fixed. The plug-in pages are now > showing versions and changelogs again:> > http://protegewiki.stanford.edu/index.php/OntoBase> > Jennifer> > >> Len Yabloko wrote:> >> > >>> I went to http://protegewiki.stanford.edu this morning 9am no versions of any plugin> >>> > > > ------------------------------> > Message: 2> Date: Thu, 23 Oct 2008 16:27:42 -0700> From: Jennifer Vendetti <vendetti at stanford.edu>> Subject: Re: [protege-discussion] FW: UMLS TAB_problems> To: User support for Core Protege and the Protege-Frames editor> <protege-discussion at mailman.stanford.edu>> Message-ID: <4901086E.6020302 at stanford.edu>> Content-Type: text/plain; charset="windows-1252"> > 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> > -------------- next part --------------> An HTML attachment was scrubbed...> URL: http://mailman.stanford.edu/pipermail/protege-discussion/attachments/20081023/34ec2fe1/attachment.htm > -------------- next part --------------> A non-text attachment was scrubbed...> Name: moz-screenshot-39.jpg> Type: image/jpeg> Size: 55268 bytes> Desc: not available> Url : http://mailman.stanford.edu/pipermail/protege-discussion/attachments/20081023/34ec2fe1/attachment.jpg > > ------------------------------> > _______________________________________________> protege-discussion mailing list> protege-discussion at lists.stanford.edu> https://mailman.stanford.edu/mailman/listinfo/protege-discussion> > > End of protege-discussion Digest, Vol 27, Issue 24> **************************************************
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