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[bioontology-support] Help Deleting Troublesome Ontologies

Jennifer Leigh Vendetti vendetti at
Thu Jul 5 11:52:27 PDT 2018

Hello Sydney,

Could you please clarify for us if you’re working on the main BioPortal, or a virtual appliance instance?


On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at<mailto:hoppesyd at>> wrote:


I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background.

Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded
message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it.

Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)

Thank you for your help!
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at<mailto:hoppesyd at> | 614.282.1314
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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