Confusion regarding entity versus admin profile declarations

[mellybelly]

Why are the DOBs or age not asserted within the "admin profile"?

from @cmungall : Every assertion about an entity is partitioned into a module, and can have full provenance/audit info attached. By separating this into its own chunk, we have the flexibility of swapping out this piece and referencing a more dedicated format. This is the same principle for representing anything that is not a phenotype. There is a dedicated PED format, but we can capture this in the packet if we need to. Same for variants.

My confusion is more about the fact that we are recording sex and type on the entity declaration, but age on the admin profile. Is the idea that you could have the same person entity in the same phenopacket at different ages? What if the sex changes? What does the sex refer to anyway - chromosomal sex or phenotypic sex? Should potentially use the new PATO classes here?

entities:

• id: "doi: 10.1101/mcs.a000661#patient1" type: human biological_sex: female

admin_profile:

• entity: "doi: 10.1101/mcs.a000661#patient1" property: age value: literal: 23 years type: age source: id: "doi: 10.1101/mcs.a000661"

[jmcmurry]

Also cc: @mbrush and @julesjacobsen Per Jules, if everything is "entity" it could cause problems in the Java implementation. We need to be able to distinguish, not just taxon, but also whether the 'entity' of that taxon represents an individual, a genotype, a strain, a population etc.