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[bioontology-support] problem with Protege import plugin

Natasha Noy noy at stanford.edu
Tue Dec 18 12:48:02 PST 2012


Hi Chris,

Here is a response from Tania Tudorache, the developer of the plugin (she is not subscribed to the list and has asked me to post):

> Hi Chris,
> 
> Unfortunately, you won't be able to import MeSH terms with the current BioPortal import plugin.  As you may have noticed, MeSH is not browsable in BioPortal because it does not have a class tree. The import plugin displays the class tree and allows you to pick the terms to import, but in the case of MeSH, this tree cannot be built.
> 
> We are working on a new version of the plugin that will allow you to also import search results (e.g. you may search MeSH for a particular term), rather than supporting only imports from the BioPortal class tree. Realistically, the new version of the plugin won't be available this year, but early next year. 
> 
> I would also recommend to update the BioPortal import plugin from the wiki. The instructions are here:
> http://protegewiki.stanford.edu/wiki/BioPortal_Import_Plugin#Download
> 
> Best regards,
> Tania
> 

Natasha




On Dec 18, 2012, at 5:21 AM, Chris Wroe wrote:

> Are there any known problems using the BioOntology import plugin in Protege 3.4.8?
> 
> I got this exception when trying to import 'atenolol' from MeSH
> 
> WARNING: Exception caught talking to bioportal -- java.io.FileNotFoundException:
> http://rest.bioontology.org/bioportal/path/46836/?source=D001262&target=root&apikey={valid key was here}
> 
> Moving to a Web Browser it also failed to retrieve the path for MeSH D001262 using that URL but the concept does seem to be there and is returned with the following Rest URL.
> 
> http://rest.bioontology.org/bioportal/concepts/46836?conceptid=D001262&apikey={valid key was here}
> 
> Thanks,
> 
> Chris
> 
> Health Informatician
> BMJ Group
> 
> 
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> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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