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updated cell_type_ontology_term_id (#1086)
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brianraymor authored Nov 5, 2024
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Expand Up @@ -476,7 +476,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
<td>categorical with <code>str</code> categories. This MUST be a CL term or <code>"unknown"</code>. It MUST be <code>"unknown"</code> when:
<ul>
<li> no appropriate term can be found (e.g. the cell type is unknown)</li>
<li><code>assay_ontology_term_id</code> is <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010961"><code>"EFO:0010961"</code></a> for <i>Visium Spatial Gene Expression</i>, <code>uns['spatial']['is_single']</code> is <code>True</code>, and the corresponding value of <code>in_tissue</code> is <code>0</code></li><br>The following terms MUST NOT be used:
<li><code>assay_ontology_term_id</code> is a descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0010961"><code>"EFO:0010961"</code></a> for <i>Visium Spatial Gene Expression</i>, <code>uns['spatial']['is_single']</code> is <code>True</code>, and the corresponding value of <code>in_tissue</code> is <code>0</code></li><br>The following terms MUST NOT be used:
<ul><li>
<a href="https://www.ebi.ac.uk/ols4/ontologies/cl/terms?obo_id=CL:0000255"><code>"CL:0000255"</code></a> for <i>eukaryotic cell</i>
</li>
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