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allow multiple donors per visium slide (#821)
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brianraymor authored Mar 22, 2024
1 parent b4ca077 commit 016b7fe
Showing 1 changed file with 5 additions and 8 deletions.
13 changes: 5 additions & 8 deletions schema/5.1.0/schema.md
Original file line number Diff line number Diff line change
Expand Up @@ -450,7 +450,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. If <code>uns['spatial']['is_single']</code> is <code>True</code>, all observations MUST be the same value. If unavailable, this MUST be <code>"unknown"</code>.
<td>categorical with <code>str</code> categories. If unavailable, this MUST be <code>"unknown"</code>.
<br><br>If <code>organism_ontolology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A9606"><code>"NCBITaxon:9606"</code></a> for <i>Homo sapiens</i>, this MUST be the most accurate HsapDv term with the following STRONGLY RECOMMENDED:
<br><br>
<table>
Expand Down Expand Up @@ -602,7 +602,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. If <code>uns['spatial']['is_single']</code> is <code>True</code>, all observations MUST be the same value. This MUST be a child of <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A33208"<code>NCBITaxon:33208</code></a> for <i>Metazoa</i>.
<td>categorical with <code>str</code> categories. This MUST be a child of <a href="https://www.ebi.ac.uk/ols4/ontologies/ncbitaxon/classes?obo_id=NCBITaxon%3A33208"<code>NCBITaxon:33208</code></a> for <i>Metazoa</i>.
</td>
</tr>
</tbody></table>
Expand All @@ -623,7 +623,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
<tr>
<th>Value</th>
<td>
categorical with <code>str</code> categories. If <code>uns['spatial']['is_single']</code> is <code>True</code>, all observations MUST be the same value. If
categorical with <code>str</code> categories. If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>,
the value MUST be formatted as one or more comma-separated (with no leading or trailing spaces) HANCESTRO
Expand Down Expand Up @@ -837,7 +837,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</tr>
<tr>
<th>Value</th>
<td>categorical with <code>str</code> categories. If <code>uns['spatial']['is_single']</code> is <code>True</code>, all observations MUST be the same value. This MUST be a child of <a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0001894">PATO:0001894</a> for <i>phenotypic sex</i> or <code>"unknown"</code> if unavailable.
<td>categorical with <code>str</code> categories. This MUST be a child of <a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0001894">PATO:0001894</a> for <i>phenotypic sex</i> or <code>"unknown"</code> if unavailable.
</td>
</tr>
</tbody></table>
Expand Down Expand Up @@ -1860,11 +1860,8 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* Added `array_col` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Added `array_row` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Updated the requirements for `cell_type_ontology_term_id` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>. The value must be `"unknown"` if the corresponding value of `in_tissue` is `0`.
* Updated the requirements for `development_stage_ontology_term_id`. All observations must be the same value when <code>uns['spatial']['is_single']</code> is <code>True</code>.
* Added `in_tissue` for _Visium Spatial Gene Expression_ when <code>uns['spatial']['is_single']</code> is <code>True</code>
* Updated the requirements for `organism_ontology_term_id`. All observations must be the same value when <code>uns['spatial']['is_single']</code> is <code>True</code>.
* Updated the requirements for `self_reported_ethnicity_ontology_term_id`. There must be no duplication of terms. All observations must be the same value when <code>uns['spatial']['is_single']</code> is <code>True</code>.
* Updated the requirements for `sex_ontology_term_id`. All observations must be the same value when <code>uns['spatial']['is_single']</code> is <code>True</code>.
* Updated the requirements for `self_reported_ethnicity_ontology_term_id`. There must be no duplication of terms.
* obsm (Embeddings)
* Added `spatial` for _Visium Spatial Gene Expression_ and _Slide-seqV2_
* Updated requirements for `X_{suffix}`. {suffix} MUST NOT be `"spatial"`.
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