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[bioontology-support] NCBO Virtual Appliance: can't connect with Protege

Ray Fergerson ray.fergerson at
Wed Sep 25 19:28:46 PDT 2013


First you need to make sure that you are using Protégé 3.X rather than
4.X. The protégé database used by BioPortal (and the VM) is a 3.X version.

The Protégé/MySQL database user and password that you need are from here:

Configuration file

This file has the following stuff:







From: bioontology-support-bounces at
[mailto:bioontology-support-bounces at] On Behalf Of
Johnson, David
Sent: Monday, September 23, 2013 6:26 AM
To: support at
Subject: [bioontology-support] NCBO Virtual Appliance: can't connect with


I'm trying to follow the instructions under 'How do I add or change
categories?' from the FAQ
(, however
I can't seem to get Protégé to connect to my VM's database. I get a
'RuntimeException. Message: Communications link failure', and it seems I
can't even telnet onto the MySQL port that I should be connecting to.

Is the VM configured in a particular way that blocks connecting from

I've tried looking for more comprehensive documentation on managing my own
instance of BioPortal (e.g. How to load/unload ontologies as an
administrator) but not found much apart front the wiki pages – a pointer
to some docs would be a great help.


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