Jim Balhoff

@turbomam PO is Plant Ontology. Coincidentally Protein Ontology also doesn't provide a base file, but I am simulating one: https://github.com/NCATS-Tangerine/ubergraph/blob/8e1a2938e4dcc1c1a104dcd0cbcd375e65a3a1a8/Makefile#L18-L24 I can temporarily do that for PO and FOODON as...

> .owl - discouraged, but default interpretation is OWL layered on RDF and serialized as Turtle(?) (or: RDF/XML, as per OBO) Most packages I'm familiar with assume that `.owl` is...

An alternative approach might be to include the prefix declarations in machine-readable form (but "reified") within the ontology rather than linking out, using the [SHACL vocabulary](https://www.w3.org/TR/shacl/#sparql-prefixes). We're using this here:...

> @balhoff totally, good idea. Would you say, just importing this with owl:imports? Yeah that sounds great.

Here's relevant output from my recent boomer run:  @sjm41 I could explain these boomer pictures on the ontology call next Monday (or sooner if you want). Any red or...

Boomer output:  @sjm41 the gray lines here indicate a subclass relationship stated by Rhea (not boomer proposals).

@pgaudet are you talking about unreleased RHEA IDs here?

@ValWood @pgaudet right now if you enter an unreleased RHEA id, this will be filtered from the release ontology build. This is fine for a regular xref, but if it...

I just want to express my support for this feature addition. I think it's what we need in the OBO ShEx file to state that a term should not have...

I think the trouble is that there are many undeclared properties used as triple objects for `owl:onProperty`. Example: ```turtle a owl:Class, linkml:ClassDefinition ; rdfs:label "CodeableConcept" ; rdfs:subClassOf [ a owl:Restriction...