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[bioontology-support] category list on BioPortal VM

Line Pouchard linepouchard at
Thu Apr 26 12:34:12 PDT 2012

Hi Paul:

Is there documentation on setting up a connection between the Protege
client and the VM?

On Thu, Apr 26, 2012 at 2:59 PM, Paul R Alexander
<palexander at> wrote:
> 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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