cellxgene-schema CLI must update validation for obs['assay_ontology_term_id']

[brianraymor]

Changelog

• obs (Cell metadata)
  • Updated the requirements for assay_ontology_term_id to include descendants of Visium Spatial Gene Expression. All observations must contain the same value. Also updated recommended values for assays.

Design

assay_ontology_term_id

Key	assay_ontology_term_id
Annotator	Curator MUST annotate.
Value	categorical with str categories. This MUST be an EFO term and either: the most accurate descendant of "EFO:0002772" for assay by molecule the most accurate descendant of "EFO:0010183" for single cell library construction If assay_ontology_term_id is either a descendant of "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2 then all observations MUST contain the same value. An assay based on 10X Genomics products SHOULD either be "EFO:0008995" for 10x technology or preferably its most accurate descendant. An assay based on SMART (Switching Mechanism at the 5' end of the RNA Template) or SMARTer technology SHOULD either be "EFO:0010184" for Smart-like or preferably its most accurate descendant. Recommended values for specific assays: For Use 10x 3' v2 "EFO:0009899" 10x 3' v3 "EFO:0009922" 10x 5' v1 "EFO:0011025" 10x 5' v2 "EFO:0009900" Smart-seq2 "EFO:0008931" Visium Spatial Gene Expression V1 "EFO:0022857" Visium CytAssist Spatial Gene Expression, 6.5mm "EFO:0022859" Visium CytAssist Spatial Gene Expression, 11mm "EFO:0022860"