From be904b30f768679601aa65e74f1a4eb5d9275fab Mon Sep 17 00:00:00 2001
From: Brian Raymor <brianraymor@chanzuckerberg.com>
Date: Tue, 3 Dec 2024 13:48:47 -0800
Subject: [PATCH] updated sex_ontology_term_id (#1145)

---
 schema/drafts/5.3.0.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/schema/drafts/5.3.0.md b/schema/drafts/5.3.0.md
index ba1cd0aba..7090d2688 100644
--- a/schema/drafts/5.3.0.md
+++ b/schema/drafts/5.3.0.md
@@ -1011,7 +1011,12 @@ If <code>organism_ontolology_term_id</code> is <code>"NCBITaxon:9606"</code> for
     </tr>
     <tr>
       <th>Value</th>
-        <td>categorical with <code>str</code> categories. This MUST be a descendant of <a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0001894">PATO:0001894</a> for  <i>phenotypic sex</i> or <code>"unknown"</code> if unavailable.
+        <td>categorical with <code>str</code> categories. This MUST be <code>"unknown"</code> if unavailable; otherwise, this MUST be one of:<br><br>
+        <ul>
+        <li><a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0000383">PATO:0000383</a> for  <i>female</i></li>
+        <li><a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0000384">PATO:0000384</a> for  <i>male</i></li>
+        <li><a href="https://www.ebi.ac.uk/ols4/ontologies/pato/classes?obo_id=PATO%3A0001340">PATO:0001340</a> for  <i>hermaphrodite</i></li>
+        </ul>
         </td>
     </tr>
 </tbody></table>
@@ -2061,7 +2066,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
   * Updated _Visium Spatial Gene Expression_ table row to _Descendants of Visium Spatial Gene Expression_
   * Added matrix requirements for _Visium CytAssist Spatial Gene Expression, 11mm_.
 * obs (Cell metadata)
-  * Updated  the requirements for `array_col`:
+  * Updated the requirements for `array_col`:
     *  MUST be annotated if the `assay_ontology_term_id` is a descendant of _Visium Spatial Gene Expression_
     * Added ranges for _Visium CytAssist Spatial Gene Expression, 6.5mm_ and _Visium CytAssist Spatial Gene Expression, 11mm_ 
   * Updated the requirements for `array_row`:
@@ -2076,6 +2081,7 @@ When a dataset is uploaded, CELLxGENE Discover MUST automatically add the `schem
   * 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_.
+  * Updated the requirements for `sex_ontology_term_id` to limit values to <i>female</i>, <i>hermaphrodite</i>, <i>male</i>, or `"unknown"`
 * obsm (Embeddings)
   * Updated the requirements for `spatial` to include descendants of  _Visium Spatial Gene Expression_ and to prohibit 'Not a Number' values. 
   * Updated the requirements for `X_{suffix}` to include descendants of  _Visium Spatial Gene Expression_.