experimental cellxgene-schema CLI must support C. elegans

[brianraymor]

Design

See schema 5.2.1. This update adds sex_ontology_term_id due to specific requirements for Caenorhabditis elegans.

Changelog

schema v5.2.1-experimental

• Required Ontologies - addressed by ontology guide must add C. elegans ontologies
  • Added C. elegans Development Ontology (WBls) release 2024-09-26 Wormbase WS295
  • Added C. elegans Gross Anatomy Ontology (WBbt) release 2024-09-24 Wormbase WS295
• Required Gene Annotations - addressed by experimental cellxgene-schema CLI must update gene references to Ensembl 113 release
  • Added Caenorhabditis elegans WBcel235 (GCA_000002985.3) Ensembl 113
  • Added Danio rerio GRCz11 (GCA_000002035.4) Ensembl 113
  • Added Drosophila melanogaster BDGP6.46 (GCA_000001215.4) Ensembl 113
• obs (Cell metadata)
  • Updated development_stage_ontology_term_id to include:
    • Caenorhabditis elegans
  • Added organism_cell_type_ontology_term_id
  • Updated organism_ontology_term_id to require all observations to contain the same value for:
    • Caenorhabditis elegans
  • Added organism_tissue_ontology_term_id
  • Updated sex_ontology_term_id for Caenorhabditis elegans
  • Updated tissue_type to require "tissue" for:
    • Caenorhabditis elegans
• var and raw.var (Gene Metadata)
  • Updated feature_reference to include:
    • Caenorhabditis elegans