Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added genetic ancestry #1117

Merged
merged 2 commits into from
Nov 19, 2024
Merged

Added genetic ancestry #1117

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a808884
Added genetic ancestry
brianraymor Nov 19, 2024
2008623
editorial
brianraymor Nov 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
177 changes: 177 additions & 0 deletions schema/drafts/5.3.0.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Loading