added Extension array to Element (#85)

examples/mappable-concept-gene.yaml

@@ -12,4 +12,7 @@ mappings:
 - coding: 
     code: "675"
     system: https://www.ncbi.nlm.nih.gov/gene/
-  relation: closeMatch
+  relation: closeMatch
+extensions:
+- name: "AlsoKnownAs"
+  value: "FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2"

schema/gks-core/def/Characteristic.rst

@@ -26,6 +26,10 @@ Some Characteristic attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - name
       - string
       - 1..1

schema/gks-core/def/Coding.rst

@@ -26,6 +26,10 @@ Some Coding attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - label
       - string
       - 0..1

schema/gks-core/def/ConceptMapping.rst

@@ -26,6 +26,10 @@ Some ConceptMapping attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - coding
       - :ref:`Coding`
       - 1..1

schema/gks-core/def/Element.rst

@@ -24,3 +24,7 @@ The base definition for all identifiable data objects.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.

schema/gks-core/def/Extension.rst

@@ -25,6 +25,10 @@ Some Extension attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - name
       - string
       - 1..1

schema/gks-core/def/MappableConcept.rst

@@ -25,6 +25,10 @@ Some MappableConcept attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - label
       - string
       - 1..1

schema/gks-core/def/RecordMetadata.rst

@@ -26,6 +26,10 @@ Some RecordMetadata attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - recordIdentifier
       - string
       - 0..1

schema/gks-core/gks-core-source.yaml

@@ -924,6 +924,18 @@ $defs:
           The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is
           unique within a given system, but may or may not be globally unique outside the system. It
           is used within a system to reference an object from another.
+      extensions:
+        type: array
+        ordered: false
+        items:
+          $ref: "#/$defs/Extension"
+        description: >-
+          A list of extensions to the Entity, that allow for capture of information not directly
+          supported by elements defined in the model.
+        $comment: >-
+          Extension objects have a key-value data structure that allows definition of custom
+          fields in the data itself. Extensions are not expected to be natively understood,
+          but may be used for pre-negotiated exchange of message attributes between systems.
 
   Coding:
     inherits: Element

schema/gks-core/json/Characteristic

@@ -11,6 +11,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "name": {
          "type": "string",
          "description": "The type of the trait  or role described by the trait (e.g. 'ethnicity', 'sex', 'age', 'disease status')."

schema/gks-core/json/Coding

@@ -10,6 +10,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "label": {
          "type": "string",
          "description": "The human-readable name for the coded concept, as defined by the code system."

schema/gks-core/json/ConceptMapping

@@ -10,6 +10,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "coding": {
          "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding",
          "description": "A structured representation of a code for a defined concept in a terminology or code system."

schema/gks-core/json/Extension

@@ -10,6 +10,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "name": {
          "type": "string",
          "description": "A name for the Extension. Should be indicative of its meaning and/or the type of information it value represents."

schema/gks-core/json/MappableConcept

@@ -10,6 +10,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "label": {
          "type": "string",
          "description": "A primary name for the concept."

schema/gks-core/json/RecordMetadata

@@ -11,6 +11,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
+      },
       "recordIdentifier": {
          "type": "string",
          "description": "The identifier of the data record or object described in this RecordMetadata object."