cellxgene-schema CLI must add validation for obs['genetic_ancestry_*']

[brianraymor]

Changelog

• obs (Cell metadata)
  • Added genetic_ancestry_African
  • Added genetic_ancestry_East_Asian
  • Added genetic_ancestry_European
  • Added genetic_ancestry_Indigenous_American
  • Added genetic_ancestry_Oceanian
  • Added genetic_ancestry_South_Asian

Design

If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then for each observation for the following fields, either all their values must be float("nan") or the sum of their values MUST be1.0:

• genetic_ancestry_African
• genetic_ancestry_East_Asian
• genetic_ancestry_European
• genetic_ancestry_Indigenous_American
• genetic_ancestry_Oceanian
• genetic_ancestry_South_Asian

genetic_ancestry_African

Key	genetic_ancestry_African
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0010" for African expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

genetic_ancestry_East_Asian

Key	genetic_ancestry_East_Asian
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0009" for East Asian expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

genetic_ancestry_European

Key	genetic_ancestry_European
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0005" for European expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

genetic_ancestry_Indigenous_American

Key	genetic_ancestry_Indigenous_American
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0013" for Indigenous American expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

genetic_ancestry_Oceanian

Key	genetic_ancestry_Oceanian
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0017" for Oceanian expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

genetic_ancestry_South_Asian

Key	genetic_ancestry_South_Asian
Annotator	Curator MUST annotate.
Value	float. All observations with the same donor_id MUST contain the same value. If organism_ontolology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan") if unavailable; otherwise, the value MUST be the genetic ancestry percentage of "HANCESTRO:0006" for South Asian expressed as a float greater than or equal to 0.0 and less than or equal to 1.0

[joyceyan]

@brianraymor Anndata doesn't seem to support allowing multiple data types in a single column. What do you think of changing the schema so that when organism is not homo sapiens, we require that the value is float('nan') instead of a string "na"?

[brianraymor]

Noted No support for mixed column type. Confirmed with @ivirshup.

[brianraymor]

@joyceyan - I updated the schema (and the top-level summary comment) with your solution. Apologies for missing the Anndata issue with pandas mixed data types.

CC: @jahilton

[joyceyan]

Thanks @brianraymor !