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updated array_col (#1083)
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brianraymor authored Nov 5, 2024
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26 changes: 24 additions & 2 deletions schema/drafts/5.3.0.md
Original file line number Diff line number Diff line change
Expand Up @@ -317,11 +317,33 @@ Curators MUST annotate the following columns in the `obs` dataframe:
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<th>Annotator</th>
<td>Curator MUST annotate if <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> and <code>uns['spatial']['is_single']</code> is <code>True</code>; otherwise, this key MUST NOT be present.</td>
<td>Curator MUST annotate if <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> and <code>uns['spatial']['is_single']</code> is <code>True</code>; otherwise, this key MUST NOT be present.</td>
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<th>Value</th>
<td><code>int</code>. This MUST be the value of the column coordinate for the corresponding spot from the <code>array_col</code> field in <code>tissue_positions_list.csv</code> or <code>tissue_positions.csv</code>. The value MUST be in the range between <code>0</code> and <code>127</code>. See <a href="https://www.10xgenomics.com/support/software/space-ranger/analysis/outputs/spatial-outputs">Space Ranger Spatial Outputs</a>.
<td><code>int</code>. This MUST be the value of the column coordinate for the corresponding spot from the <code>array_col</code> field in <code>tissue_positions_list.csv</code> or <code>tissue_positions.csv</code>. See <a href="https://www.10xgenomics.com/support/software/space-ranger/analysis/outputs/spatial-outputs">Space Ranger Spatial Outputs</a>.<br>
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<th>For Assay</th>
<th>Value MUST be in<br>the range between</th>
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<td><i>Visium Spatial Gene Expression V1</i> [<a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0022857"><code>EFO:0022857</code></a>]</td>
<td><code>0</code> and <code>127</code></td>
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<td><i>Visium CytAssist Spatial Gene Expression, 6.5mm</i> [<a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0022859"><code>EFO:0022859</code></a>]</td>
<td><code>0</code> and <code>127</code></td>
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<td><i>Visium CytAssist Spatial Gene Expression, 11mm</i> [<a href="https://www.ebi.ac.uk/ols4/ontologies/efo/classes?obo_id=EFO%3A0022860"><code>EFO:0022860</code></a>]</td>
<td><code>0</code> and <code>223</code></td>
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