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Added genetic ancestry (#1117)
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@brianraymor
brianraymor authored Nov 19, 2024
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Expand Up @@ -559,6 +559,177 @@ Curators MUST annotate the following columns in the `obs` dataframe:
</tbody></table>
<br>

If <code>organism_ontolology_term_id</code> is <code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then for each observation for the following fields, either all their values must be <code>float("nan")</code> or the sum of their values MUST be<code>1.0</code>:

* <code>genetic_ancestry_African</code>
* <code>genetic_ancestry_East_Asian</code>
* <code>genetic_ancestry_European</code>
* <code>genetic_ancestry_Indigenous_American</code>
* <code>genetic_ancestry_Oceanian</code>
* <code>genetic_ancestry_South_Asian</code>

### genetic_ancestry_African

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_African</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0010"><code>"HANCESTRO:0010"</code></a> for <i>African</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### genetic_ancestry_East_Asian

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_East_Asian</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0009"><code>"HANCESTRO:0009"</code></a> for <i>East Asian</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### genetic_ancestry_European

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_European</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0005"><code>"HANCESTRO:0005"</code></a> for <i>European</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### genetic_ancestry_Indigenous_American

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_Indigenous_American</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0013"><code>"HANCESTRO:0013"</code></a> for <i>Indigenous American</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### genetic_ancestry_Oceanian

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_Oceanian</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0017"><code>"HANCESTRO:0017"</code></a> for <i>Oceanian</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### genetic_ancestry_South_Asian

<table>
<tbody>
<tr>
<th>Key</th>
<td>genetic_ancestry_South_Asian</td>
</tr>
<tr>
<th>Annotator</th>
<td>Curator MUST annotate.</td>
</tr>
<tr>
<th>Value</th>
<td>
<code>str</code> or <code>float</code>. All observations with the same <code>donor_id</code> MUST contain the same value.<br><br>
If <code>organism_ontolology_term_id</code> is NOT
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the
value MUST be <code>"na"</code>.<br><br>If
<code>organism_ontolology_term_id</code> is
<code>"NCBITaxon:9606"</code> for <i>Homo sapiens</i>, then the value MUST be a <code>float("nan")</code> if unavailable; otherwise, the value MUST be the genetic ancestry percentage of <a href="https://www.ebi.ac.uk/ols4/ontologies/hancestro/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHANCESTRO_0006"><code>"HANCESTRO:0006"</code></a> for <i>South Asian</i> expressed as a <code>float</code> greater than or equal to <code>0.0</code> and less than or equal to <code>1.0</code>
</td>
</tr>
</tbody>
</table>
<br />

### in_tissue

<table><tbody>
Expand Down Expand Up @@ -1904,6 +2075,12 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
* Added ranges for _Visium CytAssist Spatial Gene Expression, 6.5mm_ and _Visium CytAssist Spatial Gene Expression, 11mm_
* Updated the requirements for `assay_ontology_term_id` to include descendants of _Visium Spatial Gene Expression_. All observations must contain the same value. Also updated recommended values for assays.
* Updated the requirements for `cell_type_ontology_term_id` to include descendants of _Visium Spatial Gene Expression_.
* Added <code>genetic_ancestry_African</code>
* Added <code>genetic_ancestry_East_Asian</code>
* Added <code>genetic_ancestry_European</code>
* Added <code>genetic_ancestry_Indigenous_American</code>
* Added <code>genetic_ancestry_Oceanian</code>
* Added <code>genetic_ancestry_South_Asian</code>
* Updated the requirements for `in_tissue` to include descendants of _Visium Spatial Gene Expression_.
* obsm (Embeddings)
* Updated the requirements for `spatial` to include descendants of _Visium Spatial Gene Expression_ and to prohibit 'Not a Number' values.
Expand Down

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