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[bioontology-support] category list on BioPortal VM

Paul R Alexander palexander at
Thu Apr 26 11:41:40 PDT 2012

On 4/26/12 11:36 AM, Line Pouchard wrote:
>> Instructions say: modify the Bioportal_protege project file.
> 1) if I download from the support page and modify using my own protege
> copy, which resides on a different machine than the VM, where do I
> place the modified copy in the VM tree?
You need to use a local Protege client to connect to the Virtual 
Appliance. You won't need to store the project file on the server at 
all, it is only for local use in connecting to the Appliance.
> and 2)
> Where in the tree do I find my VM original?
> just want to cut and paste the correct ip and domain
There is no original file on the Appliance, this is a totally separate 

Modifying the Protege project file will not change the categories, 
follow steps 3-8 after modifying the file and opening it in your local 
copy of Protege in order to actually make changes.

  I don't know what the IP or domain for your Appliance is, but it 
should be the same as whatever you use to access the UI or REST services.

Steps 3-8 on the instructions require you to be running Protege locally 
on your machine in order to connect to the Appliance, where you can then 
use Protege to modify the available categories. Changes will be made 
instantly (though may take a while to show up on the UI due to caching) 
and you won't need to upload anything to the Appliance in order to make 
the change.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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