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Found this ticket as I was about to report this issue myself.
I think that as well as the title, only dpo is actually being loaded into Ontobee, as I have noticed that some FBcv IDs are not resolving.
For a little more context, the 'Drosophila Phenotype Ontology' (dpo) - http://obofoundry.org/ontology/dpo.html uses FBcv identifiers, but the 'FBcv' ontology should be the 'FlyBase Controlled Vocabulary' - http://obofoundry.org/ontology/fbcv.html
dpo is available as a standalone ontology, but it is also incorporated into FBcv, so if it is only possible to load one or the other - go for FBcv.
See row 70 of the ontology table.
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