Jim Balhoff

Since #30973, these will now all be included via SKOS properties in the JSON files.

We are injecting the axiom `'has primary input' some 'isopentenyl diphosphate(3-)' EquivalentTo 'has primary input' some 'isopentenyl diphosphate'` in "biochebi". These are generated for all pH 7.3 mapped chemicals. 'isopentenyl...

> I am not 100% sure if this only applies to axioms, but arent we mostly using `rdfs:isDefinedBy`? cc [@balhoff](https://github.com/balhoff) I think so. I didn't realize there was an IAO...

We have two terms with problems when we propagate 'in taxon' over 'regulates': ## [envenomation resulting in plasminogen activation in another organism](http://purl.obolibrary.org/obo/GO_0044544) SubClassOf [Nothing](http://www.w3.org/2002/07/owl#Nothing) ## - [envenomation resulting in plasminogen...

Thanks @pgaudet looks like those changes do clear the problems.

Sorry it was kind of a terse request. I came across the support for running fully standalone python scripts, where the dependencies and python version are declared in the header...

In Phenoscape we use the Vertebrate Taxonomy Ontology (VTO) which has many taxa not in NCBI. This was assembled from a few different taxonomy sources, including NCBI, but the pipeline...

OWL API 5 seems to be on 3.x: https://github.com/owlcs/owlapi/blob/d7e997a53b470e32700de89cc610d9daf01ea769/pom.xml#L98-L102 Should we one day finally update ROBOT and Protégé to version 5, possibly breaking some plugins? 😕

Yes, Bacteria is disjoint from Eukaryota, but it is not disjoint from the union of "Plants OR Bacteria OR Euglena". So in this case neither term is more specific than...

@ValWood would you like me to do something here? Do you want to just remove that taxon constraint? I don't know anything was wrong in this case.