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cellxgene-schema must update validation for X (Matrix Layers) #1099

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brianraymor opened this issue Nov 14, 2024 · 0 comments
Open

cellxgene-schema must update validation for X (Matrix Layers) #1099

brianraymor opened this issue Nov 14, 2024 · 0 comments
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5.3 Next minor CELLxGENE schema version after 5.2 curation software

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@brianraymor
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Changelog

X (Matrix Layers)

  • Updated Visium Spatial Gene Expression table row to Descendants of Visium Spatial Gene Expression
  • Added matrix requirements for Visium CytAssist Spatial Gene Expression, 11mm.

Design

Assay "raw" required? "raw" location "normalized" required? "normalized" location
Descendant of 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 cell 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.

if assay_ontology_term_id is "EFO:0022860" for Visium CytAssist Spatial Gene Expression, 11mm, this matrix MUST contain 14336 rows; otherwise, this matrix MUST contain 4992 rows.

If the obs['in_tissue'] value is 1, then the cell MUST contain at least one non-zero value. If any obs['in_tissue'] values are 0, then at least one cell 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
@brianraymor brianraymor added curation software 5.3 Next minor CELLxGENE schema version after 5.2 labels Nov 14, 2024
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5.3 Next minor CELLxGENE schema version after 5.2 curation software
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