Update "Animal Cells" in collection 29f92179-ca10-4309-a32b-d383d80347c1

[BAevermann]

In many of the datasets within collection:29f92179-ca10-4309-a32b-d383d80347c1 there are cells labeled as "Animal Cell". These should be curated to a more granular resolution or perhaps these are really "Unknown"?

Collection Title: Longitudinal profiling of respiratory and systemic immune responses reveals myeloid cell-driven lung inflammation in severe COVID-19

Dataset Titles known to be affected: 66 years old female - Fresh PBMCs (7 days post-intubation) 74 years old female - Fresh PBMCs (8 days post-intubation) 74 years old female - Fresh PBMCs (7 days post-intubation) 74 years old female - Fresh PBMCs (3 days post-intubation) 66 years old female - Fresh PBMCs (2 days post-intubation) 82 years old female - Fresh PBMCs (1 day post-intubation) 74 years old female - Fresh PBMCs (4 days post-intubation) 66 years old female - Fresh PBMCs (3 days post-intubation) 66 years old female - Fresh PBMCs (4 days post-intubation)

Thanks,

Brian A.

[jahilton]

Currently, "unknown" is not allowed for cell_type. "This MUST be a CL term." (the inconsistency of "unknown" across fields is addressed in #218) We typically default to CL:0000003 [native cell]. I agree that some rule is needed to ensure that unknown/unannotated cells are handled consistently.

[brianraymor]

@jahilton - the original case ("animal cell") will be invalid in schema 4. Do you want to include in your 3.1 changes?

[jahilton]

@brianraymor if you're OK with it, we'll just wait until schema 4 and migrate all 'animal cell' (maybe 'somatic cell' & others too?) to 'native cell' with that migration

[jahilton]

This has been revised (and the now 'native cell' will soon go to 'unknown' in 5.0.0)