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

Johnson, David david.johnson at
Mon Sep 23 06:26:22 PDT 2013


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 outside?

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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