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mfutey merged 2 commits into from
Jun 16, 2025
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Update cap_anndata_schema.md #142

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Update cap_anndata_schema.md
mfutey Jun 13, 2025
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Update cap_anndata_schema.md
mfutey Jun 16, 2025
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40 changes: 39 additions & 1 deletion docs/cap_anndata_schema.md
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Expand Up @@ -2,7 +2,7 @@

Contact: [...]

Version: 1.0.1
Version: 1.0.2

The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "NOT RECOMMENDED" "MAY", and "OPTIONAL" in this document are to be interpreted as described in [BCP 14](https://tools.ietf.org/html/bcp14), [RFC2119](https://www.rfc-editor.org/rfc/rfc2119.txt), and [RFC8174](https://www.rfc-editor.org/rfc/rfc8174.txt) when, and only when, they appear in all capitals, as shown here.

Expand Down Expand Up @@ -930,6 +930,40 @@ For example, if the user specified the cell annotation as `broad_cells1`, then t
</tr>
</tbody></table>

### [cellannotation_setname]--confidence_score

**Format:** The column name is the string prefix `[cellannotation_setname]--` concatenated with the string value `confidence_score`, i.e. `[cellannotation_setname] + '--' + 'confidence_score'`

<table><tbody>
<tr>
<td><b>column</b></td>
<td><code>[cellannotation_set]--confidence_score</code></td>
</tr>
<tr>
<td><b>index</b></td>
<td>Cell barcode names</td>
</tr>
<tr>
<td><b>dtype</b></td>
<td>float</td>
</tr>
<tr>
<td><b>value</b></td>
<td>A float number in [0,1] range corresponding to the model's internal probability that the predicted label is correct.</td>
</tr>
<tr>
<td><b>source</b></td>
<td>file or UI</td>
</tr>
<tr>
<td><b>required for publication on CAP</b></td>
<td>no</td>
</tr>
<tr>
<td><b>example</b></td>
<td><code>0.45</code></td>
</tr>
</tbody></table>

# `var` and `raw.var` (Gene Metadata)

Expand Down Expand Up @@ -1653,3 +1687,7 @@ schema version 1.0.1
<li>Added <code>hierarchy</code> to <code>uns</code> section</li>
</ul>

schema version 1.0.2
<ul>
<li>Added <code>[cellannotation_setname]--confidence_score</code> to <code>obs</code> section</li>
</ul>