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hail shows up as a root term in ENVO #619

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cmungall opened this issue Feb 9, 2024 · 0 comments · Fixed by EnvironmentOntology/envo#1498
Closed

hail shows up as a root term in ENVO #619

cmungall opened this issue Feb 9, 2024 · 0 comments · Fixed by EnvironmentOntology/envo#1498
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@cmungall
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cmungall commented Feb 9, 2024

Describe the bug

hail unexpectedly shows up as a root class in ENVO

image

However, it should show up under "object aggregate" (which is admittedly a poor parent)

This can be seen here:

https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_03400011

image

The same for "depth of water ice"

(the other danglers as roots is also not ideal but this is ENVO's problem, not OLS's)

To Reproduce

Go here
https://www.ebi.ac.uk/ols4/ontologies/envo/

Expected behavior

"hail" should not be a root as it is transitively under "entity" which is already a roo

Screenshots
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See above

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Additional context

I have a suspicion about what the issue is. I will link to an ENVO issue that describes it. Basically I think the OLS behavior is odd if ontologies are not relaxed (in the robot sense), and they have no structure subClassOf parent, there is an entailed parent via an equivalence axiom.

This is how it looks in Protege

image

IMO no one should ever use an IntersectionOf on RHS of a subClassOf. This "shields" it from robot relax (see ontodev/robot#1183). I suspect something similar is happening oin OLS. When you are on a node, it does some kind of structural reasoning to get the parent

However, when you are on the ontology page, this structural reasoning is not involved, so hail appears as if it has no parents

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