Latest release of ENVO is declaring `rdf:type` as an annotation property

[gouttegd]

The latest release of ENVO contains the following declaration:

<!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#type -->

<owl:AnnotationProperty rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>

which declares rdf:type as an annotation property.

This has the side-effect of causing all axioms that are annotated with any annotation property, to be also annotated with an additional rdf:type annotation, as can be seen when looking at the ontology in Functional Syntax:

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0002-6601-2165>)  
                    Annotation(rdf:type owl:Axiom)
                    obo:IAO_0000115 envo:disconnected_from "A is disconnected_from B if they have no parts in common.")

...

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "USGS:SDTS")
                    Annotation(rdf:type owl:Axiom)
                    oboInOwl:hasNarrowSynonym obo:ENVO_00000020 "catch basin")

SubObjectPropertyOf(Annotation(obo:RO_0002582 "true"^^xsd:boolean)
                    Annotation(rdf:type owl:Axiom)
                    ObjectPropertyChain(obo:RO_0002507 obo:BFO_0000050) obo:RO_0002509)

...

[balhoff]

It looks like this is coming from foodon_import.owl.

[balhoff]

I think @ddooley fixed an issue related to this a while back: FoodOntology/foodon@ba40f62
Maybe just need to refresh foodon import?

[gouttegd]

What is strange is that this was fixed 1.5 years ago (February 2024), and Foodon has had several releases since then, so the fix should have been brought in already, when imports were refreshed before the 2025-08-19 release?

But instead, it is at that moment (the 2025-08-19 release) that the bogus declaration was brought in – even though by then the latest release of Foodon (2025-02-01) no longer had it.

[ddooley]

Cripes! I recall getting rdf:type as an axiom via an OntoFox import, and it was hard to resolve which ontology upstream that had this erronious code in it. So I've been stuck manually removing it from Genepio more recently, and FoodOn a while back.

Is it actual releases of ontology that are being imported into ENVO, or is it say github master/main branches or ontofox sources bringing it in?

[ddooley]

Our switch to latest ODK for both FoodOn and Genepio this year appears to have omitted that extra rdfs:type filter that blocked it from ontofox imports. I've reimplemented it there so future releases for sure won't have it. But I am puzzled since as you mentioned the fix seems to be in place on previous releases.

[turbomam]

Thanks for your attention to this. How certain are we that rdf:type as an AnnotationProperty is coming from FoodOn? That would be good news since @ddooley is responsive!

If that is the case, do you guys need anything from me, @cmungall or @pbuttigieg

If you come up with a PR I will quickly check it and fast track it for release

[balhoff]

Thanks for your attention to this. How certain are we that rdf:type as an AnnotationProperty is coming from FoodOn? That would be good news since @ddooley is responsive!

@turbomam good question—I just grepped through the source files to find it because it was a curious mystery, but probably someone actually working on this project should take a careful look.

[balhoff]

@ddooley based on your prior experience, is this a problem with OntoFox that should be addressed? Or is it more due to bad input to OntoFox?

[ddooley]

I'm pretty sure its a bad ontology source - in past I think it was CDNO but their current version doesn't seem to have rdf:type as annotation so I'm puzzled.

[gouttegd]

Already fixed by @matentzn in #1647 (by refreshing the FoodON import, and updating the ODK to be sure any new occurrence of this issue will be caught by the QC check).

I still don’t understand how the problem arose in the first place since FoodON already no longer had the bogus declaration when the imports were last refreshed, but I guess we might never know. :(