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added feature_type (#993)
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brianraymor authored Aug 21, 2024
1 parent 7679c52 commit 2606086
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21 changes: 21 additions & 0 deletions schema/5.2.0/schema.md
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Expand Up @@ -1409,6 +1409,26 @@ add the feature length.
</tbody></table>
<br>

### feature_type

<table><tbody>
<tr>
<th>Key</th>
<td>feature_type</td>
</tr>
<tr>
<th>Annotator</th>
<td>CELLxGENE Discover MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td><code>str</code>. If the <code>feature_biotype</code> is <code>"gene"</code> then this MUST be the gene type assigned to the feature identifier in <code>var.index</code>. If the <code>feature_biotype</code> is <code>"spike-in"</code> then this MUST be <code>"synthetic"</code>.<br><br>See <a href="https://www.gencodegenes.org/pages/biotypes.html ">GENCODE</a> and <a href="https://useast.ensembl.org/info/genome/genebuild/biotypes.html ">Ensembl</a> references.
</td>
</tr>
</tbody></table>
<br>


## `varm`

The size of the ndarray stored for a key in `varm` MUST NOT be zero.
Expand Down Expand Up @@ -1896,6 +1916,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* Updated `schema_version` to <code>"5.2.0"</code>
* var and raw.var (Gene metadata)
* Updated the requirements for `feature_length`. All `feature_biotypes` are now included. The calculation of the value changed from the merged length of isoforms to the median of the lengths of isoforms.
* Added `feature_type`

### schema v5.1.0

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4 changes: 4 additions & 0 deletions schema/5.2.0/seurat_encoding.md
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Expand Up @@ -233,6 +233,10 @@ This `data.frame` will have the following columns required by the schema. There
<td>feature_reference</td>
<td><code>character</code></td>
</tr>
<tr>
<td>feature_type</td>
<td><code>character</code></td>
</tr>
</tbody></table>
<br>

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