Added gender_identity field and ontology. Fixes #1409.

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
 
+## 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-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._
 

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
+### 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
 ### Sequencing ontology<a name='Sequencing ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 

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._

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-to-Male Transsexual; Agender"
+    },
+    "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: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"
+    }
+  }
+}

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/ontology/gender_identity_ontology.json",
+            "user_friendly": "Gender identity"
         }
     }
 }

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.",,

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",