cellxgene-schema CLI must add validation for obs['modality'] and update validation for X

[brianraymor]

Design

See X and modality in the schema.

X (Matrix Layers)

assay_ontology_term_id or modality	"raw" required?	"raw" location	"normalized" required?	"normalized" location
modality is "transcriptomics" and assay_ontology_term_id is NOT "EFO:0010961" for Visium Spatial Gene Expression	REQUIRED. If UMI-based assay (e.g. 10x v3, Slide-seqV2), values MUST be de-duplicated molecule counts. If non-UMI-based assay (e.g. Smart-seq2), values MUST be one of read counts (e.g. FeatureCounts) or estimated fragments (e.g. output of RSEM). Each observation MUST contain at least one non-zero value. All non-zero values MUST be positive integers stored as numpy.float32.	AnnData.raw.X unless no "normalized" is provided, then AnnData.X	STRONGLY RECOMMENDED	AnnData.X
modality is "transcriptomics" and assay_ontology_term_id is "EFO:0010961" for Visium Spatial Gene Expression	REQUIRED. Values MUST be de-duplicated molecule counts. All non-zero values MUST be positive integers stored as numpy.float32. If uns['spatial']['is_single'] is False then each observation MUST contain at least one non-zero value. If uns['spatial']['is_single'] is True then the unfiltered feature-barcode matrix (raw_feature_bc_matrix) MUST be used. See Space Ranger Feature-Barcode Matrices. This matrix MUST contain 4992 rows. If the obs['in_tissue'] value is 1, then the observation MUST contain at least one non-zero value. If any obs['in_tissue'] values are 0, then at least one observation corresponding to a obs['in_tissue'] with a value of 0 MUST contain a non-zero value.	AnnData.raw.X unless no "normalized" is provided, then AnnData.X	STRONGLY RECOMMENDED	AnnData.X
modality is "epigenomics"	NOT REQUIRED		REQUIRED	AnnData.X

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modality

Key	modality
Annotator	Curator MUST annotate.
Value	categorical with str categories. This MUST be "epigenomics" or "transcriptomics". This MUST be the correct type for the corresponding assay: For Assay MUST Use 10x multiome [EFO:0030059] "epigenomics" or "transcriptomics" 10x scATAC-seq [EFO:0030007] "epigenomics" 10x transcription profiling [EFO:0030080] and its descendants "transcriptomics" BD Rhapsody Targeted mRNA [EFO:0700004] "transcriptomics" BD Rhapsody Whole Transcriptome Analysis [EFO:0700003] "transcriptomics" CEL-seq2 [EFO:0010010] and its descendants "transcriptomics" DroNc-seq [EFO:0008720] "transcriptomics" Drop-seq [EFO:0008722] "transcriptomics" GEXSCOPE technology [EFO:0700011] "transcriptomics" inDrop [EFO:0008780] "transcriptomics" MARS-seq [EFO:0008796] "transcriptomics" mCT-seq [EFO:0030060] "transcriptomics" MERFISH [EFO:0008992] "transcriptomics" methylation profiling by high throughput sequencing [EFO:0002761] and its descendants "epigenomics" microwell-seq [EFO:0030002] "transcriptomics" Patch-seq [EFO:0008853] "transcriptomics" ScaleBio single cell RNA sequencing [EFO:0022490] "transcriptomics" scATAC-seq [EFO:0010891] "epigenomics" sci-RNA-seq [EFO:0010550] and its descendants "transcriptomics" Seq-Well [EFO:0008919] and its descendants "transcriptomics" Smart-like [EFO:0010184] and its descendants "transcriptomics" spatial transcriptomics [EFO:0008994] and its descendants "transcriptomics" SPLiT-seq [EFO:0009919] "transcriptomics" STRT-seq [EFO:0008953] "transcriptomics" TruDrop [EFO:0700010] "transcriptomics" If the assay does not appear in this table, the most appropriate value MUST be selected and the curation team informed during submission so that the assay can be added to the table.