Merge pull request #1475 from HumanCellAtlas/esv-gender-identity-Issu…

…e1409 Added gender_identity field and ontology. Fixes #1409.
HumanCellAtlas · Dec 11, 2024 · 7d8aeed · 7d8aeed
2 parents dfa1e89 + 447afb5
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diff --git 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/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
@@ -170,6 +170,17 @@ 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
 
+## 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
+
+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 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
@@ -264,6 +264,10 @@ 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
+### 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 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/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md
@@ -443,6 +443,7 @@ 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 |  | 
+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
@@ -0,0 +1,49 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "description": "A term that may be associated with a gender-related ontology term.",
+  "additionalProperties": false,
+  "required": [
+    "text"
+  ],
+  "title": "Gender identity ontology",
+  "name": "gender_identity_ontology",
+  "type": "object",
+  "properties": {
+    "describedBy" : {
+      "description": "The URL reference to the schema.",
+      "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/gender_identity_ontology",
+      "type": "string"
+    },
+    "schema_version": {
+      "description": "Version number in major.minor.patch format.",
+      "type": "string",
+      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+      "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 Gender; Agender; Non-Binary Gender"
+    },
+    "ontology": {
+      "description": "An ontology term identifier in the form prefix:accession.",
+      "type": "string",
+      "graph_restriction":  {
+        "ontologies" : ["obo:ncit"],
+        "classes": ["NCIT:C17357"],
+        "relations": ["rdfs:subClassOf"],
+        "direct": false,
+        "include_self": false
+      },
+      "user_friendly": "Gender identity ontology ID",
+      "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 Gender; Agender; Non-Binary Gender"
+    }
+  }
+}
diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json
@@ -199,6 +199,12 @@
             "type": "object",
             "$ref": "module/ontology/mass_unit_ontology.json",
             "user_friendly": "Weight unit"
+        },
+        "gender_identity": {
+            "description": "The donor's personal sense of their own gender at the time of the experiment.",
+            "type": "object",
+            "$ref": "module/ontology/gender_identity_ontology.json",
+            "user_friendly": "Gender identity"
         }
     }
 }
diff --git 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": {
@@ -45,6 +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",
                 "instrument_ontology": "5.3.6",
                 "length_unit_ontology": "5.3.5",
                 "library_amplification_ontology": "1.2.5",
@@ -94,7 +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"