Merge pull request #587 from openMetadataInitiative/lzehl_specimenUpdate

specimen set statistics via isPartOf for sets

Author: Raphael-Gazzotti

schemas/research/specimenAge.schema.tpl.json

@@ -0,0 +1,22 @@
+{
+  "_type": "core:SpecimenAge",
+  "required": [
+    "age",
+    "reference"
+  ],
+  "properties": {
+    "age": {
+      "_instruction": "Enter the age value.",
+      "_embeddedTypes": [
+        "core:QuantitativeValue",
+        "core:QuantitativeValueRange"
+      ]
+    },
+    "reference": {
+      "_instruction": "Enter the age reference for the specified age value.",
+      "_linkedTypes": [
+        "controlledTerms:AgeReference"
+      ]
+    }
+  }
+}

schemas/research/specimenState.schema.tpl.json

@@ -8,10 +8,19 @@
       "_instruction": "Enter any additional remarks concerning the specimen (set) in this state."
     },
     "age": {
-      "_instruction": "Enter the age of the specimen (set) in this state.",
+      "_instruction": "Enter the age and age reference of the specimen (set) in this state.",
       "_embeddedTypes": [
-        "core:QuantitativeValue",
-        "core:QuantitativeValueRange"
+        "core:SpecimenAge"
+      ]
+    },
+    "associatedProtocol": {
+      "type": "array",
+      "minItems": 1,
+      "uniqueItems": true,
+      "_instruction": "Add all technical and/or behavioral protocols associated with this specimen state.",
+      "_linkedTypes": [
+        "core:Protocol",
+        "core:BehavioralProtocol"
       ]
     },
     "internalIdentifier": {
@@ -40,10 +49,9 @@
       ]
     },
     "weight": {
-      "_instruction": "Enter the weight of the specimen (set) in this state.",
+      "_instruction": "Enter the weight and weight type of the specimen (set) in this state.",
       "_embeddedTypes": [
-        "core:QuantitativeValue",
-        "core:QuantitativeValueRange"
+        "core:SpecimenWeight"
       ]
     }
   }

schemas/research/specimenWeight.schema.tpl.json

@@ -0,0 +1,22 @@
+{
+  "_type": "core:SpecimenWeight",
+  "required": [
+    "type",
+    "weight"
+  ],
+  "properties": {
+    "type": {
+      "_instruction": "Enter the weight type for the specified weight value.",
+      "_linkedTypes": [
+        "controlledTerms:WeightType"
+      ]
+    },
+    "weight": {
+      "_instruction": "Enter the weight value.",
+      "_embeddedTypes": [
+        "core:QuantitativeValue",
+        "core:QuantitativeValueRange"
+      ]
+    }
+  }
+}

schemas/research/subjectGroup.schema.tpl.json

@@ -2,14 +2,24 @@
   "_type": "core:SubjectGroup",
   "_extends": "research/specimenSet.schema.tpl.json",
   "required": [
+    "numberOfSubjects",
     "studiedState"
   ],
-  "properties": {    
+  "properties": {
     "numberOfSubjects": {
       "type": "integer",
       "minimum": 2,
       "_instruction": "Enter the number of subjects that belong to this subject group."
     },
+    "isPartOf": {
+      "type": "array",
+      "minItems": 1,
+      "uniqueItems": true,
+      "_instruction": "Add all subject groups of which this subject group is a subgroup.",
+      "_linkedTypes": [
+        "core:SubjectGroup"
+      ]
+    },
     "studiedState": {
       "type": "array",
       "minItems": 1,

schemas/research/tissueSampleCollection.schema.tpl.json

@@ -15,7 +15,16 @@
       "_linkedCategories": [
         "anatomicalLocation"
       ]
-    },      
+    },     
+    "isPartOf": {
+      "type": "array",
+      "minItems": 1,
+      "uniqueItems": true,
+      "_instruction": "Add all tissue sample collections of which this tissue sample collection is a subcollection.",
+      "_linkedTypes": [
+        "core:TissueSampleCollection"
+      ]
+    },
     "laterality": {
       "type": "array",      
       "minItems": 1,