Draft updates to list of accepted assays and their categories #1405
Description
Pending Cleanup
- Inline and update Census Accepted Assays (CSV) and Census Accepted Assays Full Gene (CSV) in the schema
Before census builder consumes schema 7.0.0 datasets (still pending migration):
- Update RNA_SEQ - @brianraymor created Update assay lists in globals.py #1432
- Update ALLOWED_SPATIAL_ASSAYS - @brianraymor created Update assay lists in globals.py #1432
- Update FULL_GENE_ASSAY - @brianraymor created Update assay lists in globals.py #1432
- Remove the comments in # This list plus ALLOWED_SPATIAL_ASSAYS, should be kept in sync with docs/census_accepted_assays.csv and # This list should be kept in sync with docs/census_accepted_assays_full_gene.csv to reference the schema sections - @brianraymor created Update assay lists in globals.py #1432
- Find a new document for the non-normative assay selection guidance from the schema:
These assays were selected with the following criteria:
Only children "EFO:0002772" or "EFO:0010183" are shown as this is a constraint imposed by the CELLxGENE dataset schema >3.0.0.
- Must measure gene expression via RNA sequencing.
- Can be done at the single-cell level.
- May include nascent or elongating RNA data.
- May be targeted to specific genes in an assay-specific manner.
- May include spatial data exclusively from Visium or Slide-seq.
- Doesn't measure other non-RNA molecules concurrently.
- Doesn’t require author metadata for correct interpretability (e.g. perturbation-based technologies).
- Doesn’t intend to primarily measure RNA structure, RNA fusions, RNA modifications, or RNA interactions.
- Doesn’t intend to primarily measure non-mRNA (e.g. tRNA, rRNA, small RNAs).
- Doesn’t intend to primarily measure viral RNA.
- Doesn’t intend to primarily measure introns.
- Doesn’t do ribosome profiling.
After the draft census is published:
- Update assays not on the supported list in Contribute and Publish Data to reference the assay section in the census schema
Context
Please review and draft updates to the list of accepted assays and their categories as outlined below. Noting that a should be kept in sync design style is extremely fragile.
If there are additional references to be considered, please update this top-level summary.
Census Accepted Assays
RNA_SEQ
# list of EFO terms that correspond to RNA seq modality/measurement. These terms
# define the inclusive filter applied to obs.assay_ontology_term_id. All other
# terms are excluded from the Census.
# This list plus ALLOWED_SPATIAL_ASSAYS, should be kept in sync with docs/census_accepted_assays.csv`
ALLOWED_SPATIAL_ASSAYS
# list of EFO terms that correspond to SPATIAL modality/measurement. These terms
# define the inclusive filter applied to obs.assay_ontology_term_id. All other
FULL_GENE_ASSAY
Census Accepted Assays Full Gene (CSV)
# Full-gene assays have special handling in the "normalized" X layers
# This list should be kept in sync with docs/census_accepted_assays_full_gene.csv