Make an AbstractEntity base class for all Entities

[julesjacobsen]

(child_of: #56)

AbstractEntity should implement Entity all entity classes should extend AbstractEntity

Entity is_a ClassInstance where ClassInstance is defined as:

An abstract class for anything that can be described as a boolean combination of ontology classes

Which rather covers everything and anything. Usage of ClassInstance is not completely uniform - GenomicEntity and Publication aren't marked as ClassInstance but everything else in condition, entity, environment and evidence packages extend from ClassInstance so most likely these are omissions.

So:

1. Should GenomicEntity be a ClassInstance (I think yes, and then given that I'll create an AbstractEntity as per this ticket.)
2. Should Publication be a ClassInstance (maybe? Probably yes.)
3. Should all classes extending ClassInstance have their own @JsonldType (Probably. Again, this is sporadic in the code, but then we have issues of mismatch i.e. org.phenopackets.evidence.Publication could be associated with IAO:0000311 but is probably better less constrained as a IAO:0000310 however if not then it can be better described in ClassInstance.types)

@cmungall, @selewis, @balhoff - opinions?

[balhoff]

It seems like something should be a class instance only if you want to be able to provide a list of types and negated types. You probably wouldn't need that for Publication, right?

Currently I don't think we are doing anything with the @JsonldType annotations. We don't output @type properties for anything.

[cmungall]

negated types for publications is overkill, but it's still a class instance.

Yes, we're not using @JsonldType.

[julesjacobsen]

Might want to have a OntologyClass.notOf(id, label) builder for general negated types. Can then ask the OntologyClass if it's negated intead of adding it to a negated list.

Also consider using Decorator where Entity is decorated instead of all this inheritance on an AbstractEntity.