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restored 3.1.0 obsm requirements (#860)
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brianraymor authored Apr 26, 2024
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4 changes: 2 additions & 2 deletions schema/5.1.0/schema.md
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Expand Up @@ -1189,8 +1189,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST annotate a unique observatio
## `obsm` (Embeddings)


The size of the ndarray stored for a key in `obsm` MUST NOT be zero.

The value for each `str` key MUST be a `numpy.ndarray` of shape `(n_obs, m)`, where `n_obs` is the number of rows in `X` and `m >= 1`.

To display a dataset in CELLxGENE Explorer, Curators MUST annotate **one or more** embeddings of at least two-dimensions (e.g. tSNE, UMAP, PCA, spatial coordinates) as `numpy.ndarrays` in `obsm`.<br><br>

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* Updated the requirements for `is_primary_data` for _Visium Spatial Gene Expression_. The value must be <code>False</code>when <code>uns['spatial']['is_single']</code> is <code>False</code>.
* Updated the requirements for `self_reported_ethnicity_ontology_term_id`. There must be no duplication of terms.
* obsm (Embeddings)
* Restored v3.1.0 requirement allowing only `numpy.ndarray` values with specific shapes due to Seurat conversion failures
* Added `spatial` for _Visium Spatial Gene Expression_ and _Slide-seqV2_
* Updated requirements for `X_{suffix}`. {suffix} MUST NOT be `"spatial"`.
* uns (Dataset metadata)
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