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[bioontology-support] Question about migrating ontologies from BioPortal to local VM

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Feb 3 15:00:20 PST 2020


Hello Jahoon,


On Jan 31, 2020, at 2:01 PM, Koo, Jahoon <JAHOON.KOO at UCDENVER.EDU<mailto:JAHOON.KOO at UCDENVER.EDU>> wrote:

I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided.
It seems like some ontologies migrate with missing classes, and I don’t know what’s causing this error.
I have migrated HIVO004, FB-CV, and CHEAR ontologies, but they are missing classes and have a comment saying “No submissions available” on the web UI.
For more information, I didn’t get any http errors while running the bioportal_ontologies_import.rb script with the ontologies mentioned above.

Is there any way to fix this error?


I’m wondering if you could tell us if your ontologies have fully parsed in your appliance? You can find instructions for how to do that on our wiki:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_know_if_an_ontology_has_parsed.3F

It can take BioPortal a little bit of time to fully process all ontologies in the processing queue.

If the ontologies are fully parsed and the ontology data is still not visible in the appliance user interface, could you try flushing the cache? Instructions are available on the wiki for this as well:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_can_I_clear_the_memcached-based_UI_cache.3F

Another thing to look at if all of the above fails is to check the processing logs for each ontology for processing errors. The log files are located using the following pattern:

/srv/ncbo/repository/{ontology acronym}/{submission id}

For example, the log file for CHEAR would be located in the following directory:

/srv/ncbo/repository/CHEAR/1

Kind regards,
Jennifer

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