From e6f1b7aaae3c8c08754b60cf0a7d79dd0584c022 Mon Sep 17 00:00:00 2001
From: ESapenaVentura <sapenaventura@gmail.com>
Date: Wed, 6 Jul 2022 13:05:20 +0100
Subject: [PATCH 01/10] Added gender_identity field and ontology. Fixes #1409.

---
 docs/jsonBrowser/module.md                    | 11 +++++
 docs/jsonBrowser/required_fields.md           |  4 ++
 docs/jsonBrowser/type.md                      |  1 +
 .../ontology/gender_identity_ontology.json    | 49 +++++++++++++++++++
 .../type/biomaterial/donor_organism.json      |  6 +++
 json_schema/update_log.csv                    |  2 +
 json_schema/versions.json                     |  3 +-
 7 files changed, 75 insertions(+), 1 deletion(-)
 create mode 100644 json_schema/module/ontology/gender_identity_ontology.json

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index ee6e5195a..8155fea79 100644
--- a/docs/jsonBrowser/module.md
+++ b/docs/jsonBrowser/module.md
@@ -148,6 +148,17 @@ text | The name of a process type being used. | string | yes |  | Process type |
 ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Process type ontology ID |  | EFO:0009128; EFO:0009121
 ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Process type ontology label |  | enzymatic dissociation; blood draw
 
+## Ethnicity ontology<a name='Ethnicity ontology'></a>
+_A term that may be associated with a gender-related ontology term._
+
+Location: module/ontology/gender_identity_ontology.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+text | The gender identity of the human donor at the time of the experiment. | string | yes |  | Gender identity |  | Female-to-Male Transsexual; Agender
+ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Gender identity ontology ID |  | NCIT:C46121; NCIT:C180329
+ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Gender identity ontology label |  | Female-to-Male Transsexual; Agender
+
 ## Sequencing ontology<a name='Sequencing ontology'></a>
 _A term that may be associated with a process-related ontology term._
 
diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md
index c4c55b5ee..81c2ba2a3 100644
--- a/docs/jsonBrowser/required_fields.md
+++ b/docs/jsonBrowser/required_fields.md
@@ -248,6 +248,10 @@ text | The name of a library construction approach being used. | string |  | Lib
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
 text | The name of a process type being used. | string |  | Process type |  | enzymatic dissociation; blood draw
+### Ethnicity ontology<a name='Ethnicity ontology'></a>
+Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- 
+text | The gender identity of the human donor at the time of the experiment. | string |  | Gender identity |  | Female-to-Male Transsexual; Agender
 ### Sequencing ontology<a name='Sequencing ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md
index dd70ce41c..b6d44ee5b 100644
--- a/docs/jsonBrowser/type.md
+++ b/docs/jsonBrowser/type.md
@@ -414,6 +414,7 @@ height_unit | The unit in which Height is expressed. | object | no | [See module
 weight | Weight of organism in Weight unit. | string | no |  | Weight |  | 60; 40-60
 weight_unit | The unit in which Weight is expressed. | object | no | [See module  mass_unit_ontology](module.md/#mass_unit_ontology) | Weight unit |  | 
 timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | [See module  timecourse](module.md/#timecourse) | Timecourse |  | 
+gender_identity | The donor's personal sense of their own gender at the time of the experiment. | object | no | [See module  gender_identity_ontology](module.md/#gender_identity_ontology) | Gender identity |  | 
 
 ## Organoid
 _Information about an organoid biomaterial._
diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
new file mode 100644
index 000000000..3055d49d4
--- /dev/null
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -0,0 +1,49 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "description": "A term that may be associated with a gender-related ontology term.",
+  "additionalProperties": false,
+  "required": [
+    "text"
+  ],
+  "title": "Ethnicity ontology",
+  "name": "ethnicity_ontology",
+  "type": "object",
+  "properties": {
+    "describedBy" : {
+      "description": "The URL reference to the schema.",
+      "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/gender_identity_ontology",
+      "type": "string"
+    },
+    "schema_version": {
+      "description": "Version number in major.minor.patch format.",
+      "type": "string",
+      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+      "example": "4.6.1"
+    },
+    "text": {
+      "description": "The gender identity of the human donor at the time of the experiment.",
+      "type": "string",
+      "user_friendly": "Gender identity",
+      "example": "Female-to-Male Transsexual; Agender"
+    },
+    "ontology": {
+      "description": "An ontology term identifier in the form prefix:accession.",
+      "type": "string",
+      "graph_restriction":  {
+        "ontologies" : ["obo:hcao", "obo:ncit"],
+        "classes": ["NCIT:C17357"],
+        "relations": ["rdfs:subClassOf"],
+        "direct": false,
+        "include_self": false
+      },
+      "user_friendly": "Gender identity ontology ID",
+      "example": "NCIT:C46121; NCIT:C180329"
+    },
+    "ontology_label": {
+      "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.",
+      "type": "string",
+      "user_friendly": "Gender identity ontology label",
+      "example": "Female-to-Male Transsexual; Agender"
+    }
+  }
+}
\ No newline at end of file
diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json
index d11415adf..855bf0b24 100644
--- a/json_schema/type/biomaterial/donor_organism.json
+++ b/json_schema/type/biomaterial/donor_organism.json
@@ -184,6 +184,12 @@
             "type": "object",
             "$ref": "module/biomaterial/timecourse.json",
             "user_friendly": "Timecourse"
+        },
+        "gender_identity": {
+            "description": "The donor's personal sense of their own gender at the time of the experiment.",
+            "type": "object",
+            "$ref": "module/biomaterial/gender_identity_ontology.json",
+            "user_friendly": "Gender identity"
         }
     }
 }
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 3231ff199..052272d85 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/ontology/gender_identity_ontology,major,"Added ontology module for gender identity.",,
+type/biomaterial/donor_organism,minor,"Added non-required gender identity field.",,
diff --git a/json_schema/versions.json b/json_schema/versions.json
index 2a24a01be..256af289d 100644
--- a/json_schema/versions.json
+++ b/json_schema/versions.json
@@ -56,7 +56,8 @@
                 "sequencing_ontology": "1.1.5",
                 "species_ontology": "5.3.5",
                 "strain_ontology": "5.3.6",
-                "time_unit_ontology": "5.3.5"
+                "time_unit_ontology": "5.3.5",
+                "gender_identity_ontology": "0.0.0"
             },
             "process": {
                 "purchased_reagents": "6.1.0",

From 15e68435af4950b9efdb1b9aece6dc5dfc11a8d2 Mon Sep 17 00:00:00 2001
From: ESapenaVentura <sapenaventura@gmail.com>
Date: Wed, 6 Jul 2022 13:32:34 +0100
Subject: [PATCH 02/10] Fixed ontology class.

---
 json_schema/module/ontology/gender_identity_ontology.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
index 3055d49d4..e70349d35 100644
--- a/json_schema/module/ontology/gender_identity_ontology.json
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -30,7 +30,7 @@
       "description": "An ontology term identifier in the form prefix:accession.",
       "type": "string",
       "graph_restriction":  {
-        "ontologies" : ["obo:hcao", "obo:ncit"],
+        "ontologies" : ["obo:ncit"],
         "classes": ["NCIT:C17357"],
         "relations": ["rdfs:subClassOf"],
         "direct": false,

From 077631c61b35708d8907c79084b47c9544c7da2c Mon Sep 17 00:00:00 2001
From: ESapenaVentura <sapenaventura@gmail.com>
Date: Wed, 6 Jul 2022 14:18:05 +0100
Subject: [PATCH 03/10] Fixed typos in reference/naming

---
 docs/jsonBrowser/module.md                                | 2 +-
 docs/jsonBrowser/required_fields.md                       | 2 +-
 json_schema/module/ontology/gender_identity_ontology.json | 4 ++--
 json_schema/type/biomaterial/donor_organism.json          | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index 8155fea79..8c67c0879 100644
--- a/docs/jsonBrowser/module.md
+++ b/docs/jsonBrowser/module.md
@@ -148,7 +148,7 @@ text | The name of a process type being used. | string | yes |  | Process type |
 ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Process type ontology ID |  | EFO:0009128; EFO:0009121
 ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Process type ontology label |  | enzymatic dissociation; blood draw
 
-## Ethnicity ontology<a name='Ethnicity ontology'></a>
+## Gender identity ontology<a name='Gender identity ontology'></a>
 _A term that may be associated with a gender-related ontology term._
 
 Location: module/ontology/gender_identity_ontology.json
diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md
index 81c2ba2a3..ba7529f2b 100644
--- a/docs/jsonBrowser/required_fields.md
+++ b/docs/jsonBrowser/required_fields.md
@@ -248,7 +248,7 @@ text | The name of a library construction approach being used. | string |  | Lib
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
 text | The name of a process type being used. | string |  | Process type |  | enzymatic dissociation; blood draw
-### Ethnicity ontology<a name='Ethnicity ontology'></a>
+### Gender identity ontology<a name='Gender identity ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
 text | The gender identity of the human donor at the time of the experiment. | string |  | Gender identity |  | Female-to-Male Transsexual; Agender
diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
index e70349d35..7473e3476 100644
--- a/json_schema/module/ontology/gender_identity_ontology.json
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -5,8 +5,8 @@
   "required": [
     "text"
   ],
-  "title": "Ethnicity ontology",
-  "name": "ethnicity_ontology",
+  "title": "Gender identity ontology",
+  "name": "gender_identity_ontology",
   "type": "object",
   "properties": {
     "describedBy" : {
diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json
index 855bf0b24..e05566d9c 100644
--- a/json_schema/type/biomaterial/donor_organism.json
+++ b/json_schema/type/biomaterial/donor_organism.json
@@ -188,7 +188,7 @@
         "gender_identity": {
             "description": "The donor's personal sense of their own gender at the time of the experiment.",
             "type": "object",
-            "$ref": "module/biomaterial/gender_identity_ontology.json",
+            "$ref": "module/ontology/gender_identity_ontology.json",
             "user_friendly": "Gender identity"
         }
     }

From 276a2e93ac3197e632821470e342ea5b8be7c833 Mon Sep 17 00:00:00 2001
From: ESapenaVentura <sapenaventura@gmail.com>
Date: Thu, 17 Nov 2022 14:37:19 +0000
Subject: [PATCH 04/10] Small update on ontology pointer

---
 json_schema/module/ontology/gender_identity_ontology.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
index 7473e3476..9c80f1826 100644
--- a/json_schema/module/ontology/gender_identity_ontology.json
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -30,7 +30,7 @@
       "description": "An ontology term identifier in the form prefix:accession.",
       "type": "string",
       "graph_restriction":  {
-        "ontologies" : ["obo:ncit"],
+        "ontologies" : ["obo:hcao"],
         "classes": ["NCIT:C17357"],
         "relations": ["rdfs:subClassOf"],
         "direct": false,

From 258ca07954137452732b3fff590db89ade4a4559 Mon Sep 17 00:00:00 2001
From: ESapenaVentura <sapenaventura@gmail.com>
Date: Fri, 18 Nov 2022 09:29:42 +0000
Subject: [PATCH 05/10] Ran release_prepare.py script.

---
 changelog.md               | 8 ++++++++
 json_schema/update_log.csv | 2 --
 json_schema/versions.json  | 8 ++++----
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/changelog.md b/changelog.md
index b926cd04d..0b1ec3d90 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,6 +7,14 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
 
+### [module/ontology/gender_identity_ontology.json - v1.0.0] - 2022-11-18
+### Added
+Added ontology module for gender identity.
+
+### [type/biomaterial/donor_organism.json - v15.7.0] - 2022-11-18
+### Added
+Added non-required gender identity field.
+
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [module/protocol/matrix.json - v2.0.0] - 2022-10-31
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 052272d85..3231ff199 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -1,3 +1 @@
 Schema,Change type,Change message,Version,Date
-module/ontology/gender_identity_ontology,major,"Added ontology module for gender identity.",,
-type/biomaterial/donor_organism,minor,"Added non-required gender identity field.",,
diff --git a/json_schema/versions.json b/json_schema/versions.json
index ebdd541ff..2dbfeeae9 100644
--- a/json_schema/versions.json
+++ b/json_schema/versions.json
@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2022-10-31T11:11:44Z",
+    "last_update_date": "2022-11-18T09:20:27Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -43,6 +43,7 @@
                 "ethnicity_ontology": "5.3.9",
                 "file_content_ontology": "1.1.0",
                 "file_format_ontology": "1.0.0",
+                "gender_identity_ontology": "1.0.0",
                 "instrument_ontology": "5.3.6",
                 "length_unit_ontology": "5.3.5",
                 "library_amplification_ontology": "1.2.5",
@@ -58,8 +59,7 @@
                 "strain_ontology": "5.3.6",
                 "target_pathway_ontology": "1.0.0",
                 "time_unit_ontology": "5.3.5",
-                "treatment_method_ontology": "1.0.0",
-                "gender_identity_ontology": "0.0.0"
+                "treatment_method_ontology": "1.0.0"
             },
             "process": {
                 "purchased_reagents": "6.1.0",
@@ -91,7 +91,7 @@
             "biomaterial": {
                 "cell_line": "15.1.0",
                 "cell_suspension": "13.3.0",
-                "donor_organism": "15.6.1",
+                "donor_organism": "15.7.0",
                 "imaged_specimen": "3.3.0",
                 "organoid": "11.3.0",
                 "specimen_from_organism": "10.5.0"

From b7917e1803631f882265afea2d46e09d369af5e3 Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Fri, 22 Nov 2024 13:49:07 +0200
Subject: [PATCH 06/10] Updated ontology for gender identity

---
 json_schema/module/ontology/gender_identity_ontology.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
index 9c80f1826..7473e3476 100644
--- a/json_schema/module/ontology/gender_identity_ontology.json
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -30,7 +30,7 @@
       "description": "An ontology term identifier in the form prefix:accession.",
       "type": "string",
       "graph_restriction":  {
-        "ontologies" : ["obo:hcao"],
+        "ontologies" : ["obo:ncit"],
         "classes": ["NCIT:C17357"],
         "relations": ["rdfs:subClassOf"],
         "direct": false,

From f6f618b96b3938f7e5de443f115b6fb08a344ee6 Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Fri, 22 Nov 2024 13:50:50 +0200
Subject: [PATCH 07/10] Removed outdated version_updates

---
 changelog.md               | 8 --------
 json_schema/update_log.csv | 2 ++
 json_schema/versions.json  | 2 +-
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/changelog.md b/changelog.md
index 7b58231c3..8acf4103d 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,14 +7,6 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
 
-### [module/ontology/gender_identity_ontology.json - v1.0.0] - 2022-11-18
-### Added
-Added ontology module for gender identity.
-
-### [type/biomaterial/donor_organism.json - v15.7.0] - 2022-11-18
-### Added
-Added non-required gender identity field.
-
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [module/biomaterial/medical_history.json - v7.0.0] - 2024-11-06
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 3231ff199..5f709f2c9 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+type/biomaterial/donor_organism,minor,Added non-required gender identity field.,,
+module/ontology/gender_identity_ontology,major,Added ontology module for gender identity.,,
\ No newline at end of file
diff --git a/json_schema/versions.json b/json_schema/versions.json
index f9640754c..0b5f6bb53 100644
--- a/json_schema/versions.json
+++ b/json_schema/versions.json
@@ -45,7 +45,7 @@
                 "ethnicity_ontology": "5.3.9",
                 "file_content_ontology": "2.0.0",
                 "file_format_ontology": "1.0.0",
-                "gender_identity_ontology": "1.0.0",
+                "gender_identity_ontology": "0.0.0",
                 "instrument_ontology": "5.3.6",
                 "length_unit_ontology": "5.3.5",
                 "library_amplification_ontology": "1.2.5",

From 5efda650e0b43f08bbc95c2a486d1d58275afc4d Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Fri, 22 Nov 2024 13:54:05 +0200
Subject: [PATCH 08/10] Removed deprecated timecourse module from donor

---
 docs/jsonBrowser/type.md                         | 1 -
 json_schema/type/biomaterial/donor_organism.json | 6 ------
 2 files changed, 7 deletions(-)

diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md
index d058fdeaf..b933f9baa 100644
--- a/docs/jsonBrowser/type.md
+++ b/docs/jsonBrowser/type.md
@@ -443,7 +443,6 @@ height | Height of organism in Height unit. | string | no |  | Height |  | 160;
 height_unit | The unit in which Height is expressed. | object | no | [See module  length_unit_ontology](module.md#length-unit-ontology) | Height unit |  | 
 weight | Weight of organism in Weight unit. | string | no |  | Weight |  | 60; 40-60
 weight_unit | The unit in which Weight is expressed. | object | no | [See module  mass_unit_ontology](module.md#mass-unit-ontology) | Weight unit |  | 
-timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | [See module  timecourse](module.md#timecourse) | Timecourse |  | 
 gender_identity | The donor's personal sense of their own gender at the time of the experiment. | object | no | [See module  gender_identity_ontology](module.md#gender-identity-ontology) | Gender identity |  | 
 
 ## Organoid
diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json
index 15e2e3653..3fed10913 100644
--- a/json_schema/type/biomaterial/donor_organism.json
+++ b/json_schema/type/biomaterial/donor_organism.json
@@ -200,12 +200,6 @@
             "$ref": "module/ontology/mass_unit_ontology.json",
             "user_friendly": "Weight unit"
         },
-        "timecourse": {
-            "description": "Information relating to a timecourse associated with this biomaterial.",
-            "type": "object",
-            "$ref": "module/biomaterial/timecourse.json",
-            "user_friendly": "Timecourse"
-        },
         "gender_identity": {
             "description": "The donor's personal sense of their own gender at the time of the experiment.",
             "type": "object",

From b285f954364ddb54e1fb3fb766f126cbbbc58910 Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Fri, 22 Nov 2024 13:58:46 +0200
Subject: [PATCH 09/10] Updated outdated gender identity examples

---
 docs/jsonBrowser/module.md                                | 6 +++---
 docs/jsonBrowser/required_fields.md                       | 2 +-
 json_schema/module/ontology/gender_identity_ontology.json | 6 +++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
index a0f64089e..6ab9bf881 100644
--- a/docs/jsonBrowser/module.md
+++ b/docs/jsonBrowser/module.md
@@ -177,9 +177,9 @@ Location: module/ontology/gender_identity_ontology.json
 
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
-text | The gender identity of the human donor at the time of the experiment. | string | yes |  | Gender identity |  | Female-to-Male Transsexual; Agender
-ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Gender identity ontology ID |  | NCIT:C46121; NCIT:C180329
-ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Gender identity ontology label |  | Female-to-Male Transsexual; Agender
+text | The gender identity of the human donor at the time of the experiment. | string | yes |  | Gender identity |  | Female Gender; Agender; Non-Binary Gender
+ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Gender identity ontology ID |  | NCIT:C46110; NCIT:C205469; NCIT:C160941
+ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Gender identity ontology label |  | Female Gender; Agender; Non-Binary Gender
 
 ## Sequencing ontology<a name='Sequencing ontology'></a>
 _A term that may be associated with a process-related ontology term._
diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md
index 361fa2bc9..0078d693f 100644
--- a/docs/jsonBrowser/required_fields.md
+++ b/docs/jsonBrowser/required_fields.md
@@ -267,7 +267,7 @@ text | The name of a process type being used. | string |  | Process type |  | en
 ### Gender identity ontology<a name='Gender identity ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
-text | The gender identity of the human donor at the time of the experiment. | string |  | Gender identity |  | Female-to-Male Transsexual; Agender
+text | The gender identity of the human donor at the time of the experiment. | string |  | Gender identity |  | Female Gender; Agender; Non-Binary Gender
 ### Sequencing ontology<a name='Sequencing ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
diff --git a/json_schema/module/ontology/gender_identity_ontology.json b/json_schema/module/ontology/gender_identity_ontology.json
index 7473e3476..3187f70f2 100644
--- a/json_schema/module/ontology/gender_identity_ontology.json
+++ b/json_schema/module/ontology/gender_identity_ontology.json
@@ -24,7 +24,7 @@
       "description": "The gender identity of the human donor at the time of the experiment.",
       "type": "string",
       "user_friendly": "Gender identity",
-      "example": "Female-to-Male Transsexual; Agender"
+      "example": "Female Gender; Agender; Non-Binary Gender"
     },
     "ontology": {
       "description": "An ontology term identifier in the form prefix:accession.",
@@ -37,13 +37,13 @@
         "include_self": false
       },
       "user_friendly": "Gender identity ontology ID",
-      "example": "NCIT:C46121; NCIT:C180329"
+      "example": "NCIT:C46110; NCIT:C205469; NCIT:C160941"
     },
     "ontology_label": {
       "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.",
       "type": "string",
       "user_friendly": "Gender identity ontology label",
-      "example": "Female-to-Male Transsexual; Agender"
+      "example": "Female Gender; Agender; Non-Binary Gender"
     }
   }
 }
\ No newline at end of file

From 447afb5b2b98a425cb7b72428a1024c7a8b70443 Mon Sep 17 00:00:00 2001
From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com>
Date: Wed, 11 Dec 2024 09:30:10 +0000
Subject: [PATCH 10/10] Ran release_prepare.py script.

---
 changelog.md               | 8 ++++++++
 json_schema/update_log.csv | 2 --
 json_schema/versions.json  | 6 +++---
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/changelog.md b/changelog.md
index 8acf4103d..0105b3a6d 100644
--- a/changelog.md
+++ b/changelog.md
@@ -7,6 +7,14 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
 
+### [type/biomaterial/donor_organism.json - v17.1.0] - 2024-12-11
+### Added
+Added non-required gender identity field.
+
+### [module/ontology/gender_identity_ontology.json - v1.0.0] - 2024-12-11
+### Added
+Added ontology module for gender identity.
+
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [module/biomaterial/medical_history.json - v7.0.0] - 2024-11-06
diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv
index 5f709f2c9..3231ff199 100644
--- a/json_schema/update_log.csv
+++ b/json_schema/update_log.csv
@@ -1,3 +1 @@
 Schema,Change type,Change message,Version,Date
-type/biomaterial/donor_organism,minor,Added non-required gender identity field.,,
-module/ontology/gender_identity_ontology,major,Added ontology module for gender identity.,,
\ No newline at end of file
diff --git a/json_schema/versions.json b/json_schema/versions.json
index 0b5f6bb53..35789f50b 100644
--- a/json_schema/versions.json
+++ b/json_schema/versions.json
@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2024-11-06T17:01:14Z",
+    "last_update_date": "2024-12-11T09:29:09Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -45,7 +45,7 @@
                 "ethnicity_ontology": "5.3.9",
                 "file_content_ontology": "2.0.0",
                 "file_format_ontology": "1.0.0",
-                "gender_identity_ontology": "0.0.0",
+                "gender_identity_ontology": "1.0.0",
                 "instrument_ontology": "5.3.6",
                 "length_unit_ontology": "5.3.5",
                 "library_amplification_ontology": "1.2.5",
@@ -95,7 +95,7 @@
             "biomaterial": {
                 "cell_line": "16.0.0",
                 "cell_suspension": "14.0.0",
-                "donor_organism": "17.0.0",
+                "donor_organism": "17.1.0",
                 "imaged_specimen": "3.5.0",
                 "organoid": "11.5.0",
                 "specimen_from_organism": "10.9.0"