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[bioontology-support] category list on BioPortal VM

Paul R Alexander palexander at
Thu Apr 26 11:59:17 PDT 2012

You can run the Protege client on any machine that has access to the 
Virtual Appliance. It does not need to be run on the Appliance itself.

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

On 4/26/12 11:55 AM, Line Pouchard wrote:
> Hi Paul:
> Is there any other way than using a local Protege client?  This is not
> really an option for our install where I only use cli.
> Line
> On Thu, Apr 26, 2012 at 2:41 PM, Paul R Alexander
> <palexander at> wrote:
>> 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
>> process.
>> 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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