diff --git a/schema/5.1.0/schema.md b/schema/5.1.0/schema.md index 198cd403..2f55f4a7 100644 --- a/schema/5.1.0/schema.md +++ b/schema/5.1.0/schema.md @@ -367,6 +367,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
  • the most accurate descendant of "EFO:0010183" for single cell library construction
  • + If assay_ontology_term_id is either "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:

    @@ -1872,6 +1873,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem * obs (Cell metadata) * Added `array_col` for _Visium Spatial Gene Expression_ when uns['spatial']['is_single'] is True * Added `array_row` for _Visium Spatial Gene Expression_ when uns['spatial']['is_single'] is True + * Updated the requirements for `assay_ontology_term_id` for _Visium Spatial Gene Expression_ and _Slide-seqV2_. All observations must contain the same value. * Updated the requirements for `cell_type_ontology_term_id` for _Visium Spatial Gene Expression_ when uns['spatial']['is_single'] is True. The value must be `"unknown"` if the corresponding value of `in_tissue` is `0`. * Added `in_tissue` for _Visium Spatial Gene Expression_ when uns['spatial']['is_single'] is True * Updated the requirements for `is_primary_data` for _Visium Spatial Gene Expression_. The value must be Falsewhen uns['spatial']['is_single'] is False.