fbastian

Same problem, IMO fixing this bug should be high priority.

One of the problems is that, in composite-metazoan.owl, there is absolutely no EC axioms to owl:Nothing. They are present in ext.owl.

EC axioms to owl:Nothing still absent from composite-metazoan.owl, and present in ext.owl.

Note that these relations are not always present in the species-specific ontology, e.g. UBERON:0000074 is_a UBERON:0005325 is not present in zfa.

Hmm, interesting. Is this documented somewhere? And why is it not done using EquivalentClasses with IntersectionOf (UBERON:xxx and part_of NCBITaxon:xxx)? Don't remove them, I think I can quite easily filter...

I note here the new cycles I identified related to this issue, to make sure they are correct, and for reference for future updates of Bgee (it was very helpful...

New ones: ``` [Term] id: UBERON:0001083 name: myocardium of ventricle is_a: UBERON:0018649 {gci_relation="part_of", gci_filler="NCBITaxon:7954"} ! cardiac muscle tissue of ventricle [Term] id: UBERON:0002302 name: myocardium of atrium is_a: UBERON:0004490 {gci_relation="part_of",...

No problem, I report them all here for our pipeline, we can't accept cycles in Bgee for now. Other ones: ``` [Term] id: UBERON:0000474 name: female reproductive system is_a: UBERON:0000992...

Also, we have ``` [Term] id: UBERON:0001135 name: smooth muscle tissue is_a: WBbt:0005780 {gci_relation="part_of", gci_filler="NCBITaxon:6237"} ! non-striated muscle (C elegans) ``` While I think WBbt:0005780 should be is_a UBERON:0001135. The...

Some of them are removed by default: ``` "evolved_from", "homologous_to", "evolved_multiple_times_in", //"shares ancestor with" "RO:0002158" ```