Restore genetic ancestry

[brianraymor]

Pending

Data readiness to be assessed during 2025 Q2 planning to finalize the addition of this feature in schema 6.0.0.

Per @jahilton's suggestions:

• Should clarify that these are generated by CZI's pipeline & include links to documentation
• Update annotators to include Curator, Curator or Submitter, CELLxGENE Discover.

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March 3 2025

A recent HANCESTRO release has added an " ancestry" suffix to some of the labels in the original schema draft such as "European ancestry". Editorial updates to the text below are dependent on updating the pinned HANCESTRO release in coordination with this issue. Currently, this is blocked by data corpus conflicts with Update self_reported_ethnicity_term_id.

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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_ontology_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 be 1.0 ± 0.0002:

• 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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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_ontology_term_id is NOT "NCBITaxon:9606" for Homo sapiens, then the value MUST be a float("nan"). If organism_ontology_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