fix: address comments from vrs 2.0.0 community review ballot

docs/source/appendices/design_decisions.rst

@@ -10,7 +10,7 @@ GA4GH Inherent Properties over Value Objects
 
 In VRS 1.0 we operated under the principle that all identifiable objects in VRS (e.g. Allele, SequenceLocation, etc.)
 would be *value objects*. This meant that they should be immutable and contain only required fields that are
-necessary to uniquely identify the object. This approach somewhat simplified the ability to genertate the digests by
+necessary to uniquely identify the object. This approach somewhat simplified the ability to generate the digests by
 allowing the computation of the digest to be based on the entire object. An exception was made for properties with a
 leading underscore (namely, the *_id* property), which was removed from the object before a digest was calculated.
 

docs/source/concepts/SystemicVariation/CopyNumberChange.rst

@@ -0,0 +1,31 @@
+.. _CopyNumberChange:
+
+Copy Number Change
+!!!!!!!!!!!!!!!!!!
+
+A copy number change is used to represent the change in copy number of a sequence in a genome.
+
+Definition and Information Model
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+
+.. include::  ../../def/vrs/CopyNumberChange.rst
+
+Example
+@@@@@@@
+
+.. code-block:: json
+
+  {
+    "id": "ga4gh:CX.2_fT_6-IpUm5aS0wp8ZAkJ01MCE569L2",
+    "type": "CopyNumberChange",
+    "copyChange": "EFO:0030071",
+    "location": {
+      "sequenceReference": {
+        "refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
+        "type": "SequenceReference"
+      },
+      "end": 44909393,
+      "start": 44905795,
+      "type": "SequenceLocation"
+    }
+  }

docs/source/concepts/SystemicVariation/CopyNumberCount.rst

@@ -0,0 +1,35 @@
+.. _CopyNumberCount:
+
+Copy Number Count
+!!!!!!!!!!!!!!!!!
+
+
+A copy number count is used to represent the integer number of copies of
+a :ref:`SequenceLocation` in a genome.
+
+Definition and Information Model
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+
+.. include::  ../../def/vrs/CopyNumberCount.rst
+
+.. _CopyNumberCount:
+
+Example
+@@@@@@@
+
+.. code-block:: json
+
+  {
+    "id": "ga4gh:CN.ezEUXykQvIhX8jHADILwC9f8k-jp8tZC",
+    "type": "CopyNumberCount",
+    "copies": [3, null],
+    "location": {
+      "sequenceReference": {
+        "refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
+        "type": "SequenceReference"
+      },
+      "end": 44909393,
+      "start": 44905795,
+      "type": "SequenceLocation"
+    }
+  }

docs/source/concepts/SystemicVariation/index.rst

@@ -3,11 +3,10 @@
 Systemic Variation
 !!!!!!!!!!!!!!!!!!
 
-VRS currently covers many classes of variation that are defined on a contiguous molecule such as single nucleotide
-variants (SNVs), multi-nucleotide variants (MNVs), indels, repeats, haplotypes, breakpoints, and sequence
-rearrangements that form derivative molecules.
+VRS currently covers many classes of variation that are defined on multiple molecules
+in the context of a system, e.g. a genome, sample, or homologous chromosomes.
 
-Collectively, these types of variation are called molecular variation.
+Collectively, these types of variation are called systemic variation.
 
 .. include::  ../../def/vrs/SystemicVariation.rst
 
@@ -16,4 +15,5 @@ Collectively, these types of variation are called molecular variation.
 .. toctree::
    :titlesonly:
 
-   CopyNumber
+   CopyNumberCount
+   CopyNumberChange

docs/source/conventions/computed_identifiers.rst

@@ -266,8 +266,8 @@ However, as described here, these identifiers are dependent upon the structure o
 the identifier is constructed. Consequently, there is no guarantee that VRS computed identifiers will
 remain stable across major version releases of VRS; for example, all VRS v1.x computed identifiers are
 distinct from all VRS v2.x identifiers. It is recommended that implementers heed the maturity level of
-data classes as defined by the :ref:`maturity-model` when gauging the stability of data classes–and
-therefore object identifiers from thoses classes–across releases of VRS.
+data classes as defined by the :ref:`maturity-model` when gauging the stability of data classes-and
+therefore object identifiers from those classes-across releases of VRS.
 
 References
 @@@@@@@@@@

schema/vrs/def/Ga4ghIdentifiableObject.rst

@@ -23,7 +23,7 @@ An object for which a GA4GH computed identifier can be created.
 
 **Information Model**
 
-Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks-core:Entity`.
+Some Ga4ghIdentifiableObject attributes are inherited from :ref:`Entity`.
 
 .. list-table::
    :class: clean-wrap

schema/vrs/def/SequenceExpression.rst

@@ -23,7 +23,7 @@ An expression describing a :ref:`Sequence`.
 
 **Information Model**
 
-Some SequenceExpression attributes are inherited from :ref:`gks-core:Entity`.
+Some SequenceExpression attributes are inherited from :ref:`Entity`.
 
 .. list-table::
    :class: clean-wrap

schema/vrs/def/SequenceReference.rst

@@ -23,7 +23,7 @@ A sequence of nucleic or amino acid character codes.
 
 **Information Model**
 
-Some SequenceReference attributes are inherited from :ref:`gks-core:Entity`.
+Some SequenceReference attributes are inherited from :ref:`Entity`.
 
 .. list-table::
    :class: clean-wrap

schema/vrs/def/TraversalBlock.rst

@@ -23,7 +23,7 @@ A component used to describe the orientation of applicable molecular variation w
 
 **Information Model**
 
-Some TraversalBlock attributes are inherited from :ref:`gks-core:Entity`.
+Some TraversalBlock attributes are inherited from :ref:`Entity`.
 
 .. list-table::
    :class: clean-wrap