From 6aeb06ffebea6284c7b57f569b981bd08d4a081c Mon Sep 17 00:00:00 2001
From: Michael Baudis <675030+mbaudis@users.noreply.github.com>
Date: Mon, 19 Jun 2023 13:11:35 +0200
Subject: [PATCH] Update entryTypeDefinition.json

---
 .../json/configuration/entryTypeDefinition.json  | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/framework/json/configuration/entryTypeDefinition.json b/framework/json/configuration/entryTypeDefinition.json
index 434bebcf6..13c094cc1 100644
--- a/framework/json/configuration/entryTypeDefinition.json
+++ b/framework/json/configuration/entryTypeDefinition.json
@@ -1,14 +1,13 @@
 {
-    "$comment": "TO DO: The tagged parts should reference to `common/ontologizedElement.json`. But that configuration fails to validate. Further investigation is required, but should not affect the resulting schema.",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "additionalProperties": true,
-    "description": "Definition of an element or entry type including the Beacon v2 required and suggested attributes. This schema purpose is to  describe each type of entities included in a Beacon, hence Beacon clients could have some metadata about such entities.\n\nThe `id` attribute is the key that should be used in other parts of the Beacon Model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that fully describe an entry type.",
+    "description": "Definition of an element or entity, to describe each type of entity included in a beacon. The `id` attribute is the key that should be used in other parts of the data model to allow Beacon clients to identify the different parts (e.g. endpoints, filteringTerms, request parameters, etc.) that relvant for an entity.",
     "properties": {
         "$schema": {
             "$ref": "../common/beaconCommonComponents.json#/definitions/$schema"
         },
         "aCollectionOf": {
-            "description": "If the entry type is a collection of other entry types, (e.g. a Dataset is a collection of Records), then this attribute must list the entry types that could be included. One collection type could be defined as included more than one entry type (e.g. a Dataset could include Individuals or Genomic Variants), in such cases the entries are alternative, meaning that a given instance of this entry type could be of only one of the types (e.g. a given Dataset contains Individuals, while another Dataset could contain Genomic Variants, but not both at once).",
+            "description": "If the entry type is a collection of other entities, (e.g. a Dataset is a collection of Records), then this attribute must list the entities that can be included. One _collection_ can include more than one entity  (e.g. a Dataset in teh Beacon cdefault model could include Individuals, Biosamples, GenomicVariations, Analyses amnd Runs). In such cases in each individual response (e.g. `resultSetsResponse` of collections of type \"dataset\") will contain entries of a single entity type (e.g. biosamples) even if a dataset may contain records of multiple types.",
             "includedConcepts": {
                 "$ref": "../common/basicElement.json",
                 "type": "array"
@@ -30,13 +29,17 @@
             "type": "string"
         },
         "filteringTerms": {
-            "$comment": "TO DO: Double-check the proper way of referencing a path or relative path. 'format: uri' is throwing validation errors for relative file paths",
-            "description": "Reference to the file with the list of filtering terms that could be used to filter this concept in this instance of Beacon. The referenced file could be used to populate the `filteringTerms`endpoint. Having it independently should allow for updating the list of accepted filtering terms when it is necessary.",
+            "$comment": "TO DO: Evaluate switch this to `url` or a more specific way for allowing URLs and local file paths (is this necessary?).",
+            "description": "Reference to the list of filtering terms that could be used to filter records of this entity in this beacon.",
             "type": "string"
         },
         "id": {
-            "$comments": "++++++ THIS IS THE START OF THE ontologized element ++++++",
             "description": "A (unique) identifier of the element.",
+            "examples": [
+                "biosample",
+                "individual",
+                "dataset"
+            ],
             "type": "string"
         },
         "name": {
@@ -47,7 +50,6 @@
             "$ref": "../common/beaconCommonComponents.json#/definitions/NonFilteredQueriesAllowed"
         },
         "ontologyTermForThisType": {
-            "$comments": "++++++ THIS IS THE END OF THE ontologized element ++++++",
             "$ref": "../common/ontologyTerm.json"
         },
         "partOfSpecification": {