Add doc for how species vs. organism instances are represented

[mellybelly]

We run into the usual problem of what is the unit that can be annotated with a phenopacket.
It isn't clear in our documentation that what is intended are instances - either individual (patient, voucher specimen) or groups of individual organisms (cohort, population).

That said, is it possible to use a phenopacket to annotate a whole species/taxon? The relationship between a phenopacket and species vs. individuals should be clarified and declarative.

[cmungall]

Yes, this could be improved

Current implementing classes here:

http://static.javadoc.io/org.phenopackets/phenopackets-api/0.0.5/org/phenopackets/api/model/entity/Entity.html