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cellxgene-schema CLI must update validation for obsm['X_{suffix}'] #1106

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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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Changelog

  • obsm (Embeddings)
    • Updated the requirements for X_{suffix} to include descendants of Visium Spatial Gene Expression.

Design

X_{suffix}

Key X_{suffix} with the following requirements:

  • {suffix} MUST be at least one character in length.
  • The first character of {suffix} MUST be a letter of the alphabet and the remaining characters MUST be alphanumeric characters, '_', '-', or '.' (This is equivalent to the regular expression pattern "^[a-zA-Z][a-zA-Z0-9_.-]*$".)
  • {suffix} MUST NOT be "spatial".

{suffix} is presented as text to users in the Embedding Choice selector in CELLxGENE Explorer so it is STRONGLY RECOMMENDED that it be descriptive.

See also default_embedding in uns.
Annotator Curator MUST annotate if assay_ontology_term_id is neither a descendant of "EFO:0010961" for Visium Spatial Gene Expression nor "EFO:0030062" for Slide-seqV2.

Curator MAY annotate if assay_ontology_term_id is either a descendant of "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2.
Value numpy.ndarray with the following requirements


@brianraymor brianraymor added curation software 5.3 Next minor CELLxGENE schema version after 5.2 labels Nov 14, 2024
@joyceyan joyceyan self-assigned this Nov 18, 2024
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