This is the ontobio implementation for gorule-0000061.
The only thing tricky about this was handling identifying which tree of the ontology a GO term belonged to. In general I use the OIO:hasOBONamespace which is consistently defined for the ontology today.
But mostly in tests, there are some json ontologies that do not use this to identify the "namespace" of a term. I have chosen to think of a missing namespace as essentially "missing ontology". Presently, in the rules, the policy is to automatically pass any rule that does not have an attached ontology. This way rules that rely on the ontology can just be skipped if one isn't provided for whatever reason. The option to provide an ontology has been pretty historical in the code, although more current tooling requires an ontology in general. But some use cases w/out an ontology are still valid.
If we don't want to pass the rule if the hasOBONamespace is not defined, we would have to actually perform a subclass check which could represent some performance issues. If we need to go down that road, let us, but for now I've chosen to avoid it.
This is the ontobio implementation for gorule-0000061.
The only thing tricky about this was handling identifying which tree of the ontology a GO term belonged to. In general I use the
OIO:hasOBONamespacewhich is consistently defined for the ontology today.But mostly in tests, there are some json ontologies that do not use this to identify the "namespace" of a term. I have chosen to think of a missing namespace as essentially "missing ontology". Presently, in the rules, the policy is to automatically pass any rule that does not have an attached ontology. This way rules that rely on the ontology can just be skipped if one isn't provided for whatever reason. The option to provide an ontology has been pretty historical in the code, although more current tooling requires an ontology in general. But some use cases w/out an ontology are still valid.
If we don't want to pass the rule if the
hasOBONamespaceis not defined, we would have to actually perform a subclass check which could represent some performance issues. If we need to go down that road, let us, but for now I've chosen to avoid it.