While we have not performed testing with the OntoPortal Virtual Appliance, we expect there is an upper limit to the size of ontology that can be ingested.
(On BioPortal, we have trouble ingesting an ontology above 1.5 GB.)
We have found that converting the ontology to TTL format can reduce its size, and makes some ontologies manageable that otherwise can not be processed.
We provide further information on troubleshooting submissions of large ontologies in the Troubleshooting Submissions page.
An ontology that does not have easily discovered root classes—for example, because it is not hierarchical, doesn’t use typical hierarchical relations, or has loops in its parent hierarchy—will not be displayable in the Ontology Classes tree.
Likewise, an ontology that has a large number of classes and very few layers to its hierarchy is considered ‘flat’, and will not be displayed in the Ontology Classes tree.
Ontologies in SKOS format must be formatted in a particular way to be displayed properly in BioPortal. Please see the BioPortal SKOS Support page for more details.