Added collection_institute in specimen_from_organism.Fix#1606

docs/jsonBrowser/module.md

@@ -482,6 +482,17 @@ dlco_predicted_percent | Indicate the percentage of the predicted DLCO, based on
 kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available. | number | no |  | KCO |  | 5; 6; 4.5
 kco_predicted_percent | Indicate the percentage of the predicted KCO, based on patient demographics, if available. | number | no |  | KCO percent of predicted |  | 90; 98; 85
 
+## Collection institute<a name='Collection institute'></a>
+_Information about collection institute location._
+
+Location: module/biomaterial/collection_institute.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+latitude | The latitute of the collection institute, in decimal degrees. | string | no |  | Collection institute latitude |  | 52.1; -0.127541; 38.045956
+longitude | The longitude of the collection institute, in decimal degrees. | string | no |  | Collection institute longitude |  | 0.1; -84.512016; 23.792138
+name | The name of the collection institute. | string | no |  | Collection institute name |  | University of California, San Francisco
+
 ## Disease profile<a name='Disease profile'></a>
 _Information about specific diseases profile of the individual._
 

docs/jsonBrowser/required_fields.md

@@ -360,6 +360,8 @@ _There are no required properties in schema Human-specific_
 _There are no required properties in schema Growth conditions_
 ### Medical tests<a name='Medical tests'></a>
 _There are no required properties in schema Medical tests_
+### Collection institute<a name='Collection institute'></a>
+_There are no required properties in schema Collection institute_
 ### Disease profile<a name='Disease profile'></a>
 _There are no required properties in schema Disease profile_
 ### Preservation and storage<a name='Preservation and storage'></a>

docs/jsonBrowser/type.md

@@ -355,6 +355,7 @@ adjacent_diseases | Short description of the disease(s) adjacent to the specimen
 state_of_specimen | State of the specimen at the time of collection. | object | no | [See module  state_of_specimen](module.md#state-of-specimen) | State of specimen |  | 
 preservation_storage | Information about how a specimen was preserved and/or stored over a period of time. | object | no | [See module  preservation_storage](module.md#preservation-storage) | Preservation/Storage |  | 
 collection_time | When the biomaterial was collected. | string | no |  | Time of collection |  | 2016-01-21T00:00:00Z; 2016-03
+collection_institute | Institute where the biomaterial was collected on. | object | no | [See module  organ_ontology](module.md#organ-ontology) | Collection institute |  | 
 purchased_specimen | Information about a purchased specimen. | object | no | [See module  purchased_reagents](module.md#purchased-reagents) | Purchased specimen |  | 
 
 ## Cell suspension

json_schema/module/biomaterial/collection_institute.json

@@ -0,0 +1,44 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "description": "Information about collection institute location.",
+    "additionalProperties": false,
+    "title": "Collection institute",
+    "name": "collection_institute",
+    "type": "object",
+    "properties": {
+        "describedBy": {
+          "description": "The URL reference to the schema.",
+          "type": "string",
+          "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/familial_relationship"
+        },
+        "schema_version": {
+          "description": "The version number of the schema in major.minor.patch format.",
+          "type": "string",
+          "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+          "example": "4.6.1"
+        },
+        "latitude": {
+          "description": "The latitute of the collection institute, in decimal degrees.",
+          "type": "string",
+          "pattern": "^-?([0-8]?\\d|90)(\\.\\d{1,6})?$",
+          "example": "52.1; -0.127541; 38.045956",
+          "user_friendly": "Collection institute latitude",
+          "guidelines": "Use one decimal place to keep the exact location private."
+        },
+        "longitude": {
+          "description": "The longitude of the collection institute, in decimal degrees.",
+          "type": "string",
+          "pattern": "^-?((1?[0-7]?\\d)|180)(\\.\\d{1,6})?$",
+          "example": "0.1; -84.512016; 23.792138",
+          "user_friendly": "Collection institute longitude",
+          "guidelines": "Use one decimal place to keep the exact location private."
+        },
+        "name": {
+          "description": "The name of the collection institute.",
+          "type": "string",
+          "example": "University of California, San Francisco",
+          "user_friendly": "Collection institute name",
+          "guidelines": "Use pseudonymized name of the institute to keep the location private."
+        }
+    }
+}

json_schema/type/biomaterial/specimen_from_organism.json

@@ -117,6 +117,12 @@
                  }
               ]
         },
+        "collection_institute": {
+            "description": "Institute where the biomaterial was collected on.",
+            "type": "object", 
+            "$ref": "module/ontology/organ_ontology.json",
+            "user_friendly": "Collection institute"
+        },
         "purchased_specimen": {
             "description": "Information about a purchased specimen.",
             "type": "object",

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+module/biomaterial/collection_institute,major,"Added collection_institute module.Issue1606",,
+type/biomaterial/specimen_from_organism,minor,"Added optional collection_institute in specimen_from_organism.Issue1606",,

json_schema/versions.json

@@ -21,6 +21,7 @@
         "module": {
             "biomaterial": {
                 "cell_morphology": "6.1.7",
+                "collection_institute": "0.0.0",
                 "death": "5.5.1",
                 "disease_profile": "1.0.0",
                 "familial_relationship": "6.0.3",