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phenopackets / phenopacket-format

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Add doc for how species vs. organism instances are represented #80

Open mellybelly opened 7 years ago

mellybelly commented 7 years ago

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 commented 7 years ago

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