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[bioontology-support] problem with Protege import plugin

Chris Wroe chris.j.wroe at gmail.com
Wed Dec 19 01:22:10 PST 2012


Hi Natasha, Tania,

Thanks for your help. It makes sense now. I've successfully built the
plugin from source and it is working well. I'll post any further feedback
to the Protege mailing list.

Chris

On 18 December 2012 20:48, Natasha Noy <noy at stanford.edu> wrote:

> 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={validkey 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={validkey was here}
> >
> > Thanks,
> >
> > Chris
> >
> > Health Informatician
> > BMJ Group
> >
> >
> > _______________________________________________
> > bioontology-support mailing list
> > bioontology-support at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
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