Issue 640 (#643)

* fix #640: updated `copyChange` enumerations.
* updated CODEOWNERS
* updated schema `$id`s to 2.0.1
* init 2.0.1 change log

---------

Co-authored-by: Alex H. Wagner, PhD <[email protected]>

Author: larrybabb

.github/CODEOWNERS

@@ -1,2 +1,2 @@
 # Each line is a file pattern followed by one or more owners.
-*  @andreasprlic @ahwagner @larrybabb
+*  @ahwagner @larrybabb

docs/source/releases/2.0.rst

@@ -14,3 +14,11 @@ Major Changes
   * supports structural variation
   * imports from the GKS-core library for cross-specification alignment
   * renames Haplotype to CisPhasedBlock
+
+2.0.1
+@@@@@
+
+Summary of Changes
+##################
+
+  * updates :ref:`CopyNumberChange` draft to use named enum in lieu of MappableConcept

schema/vrs/def/CopyNumberChange.rst

@@ -92,6 +92,6 @@ Some CopyNumberChange attributes are inherited from :ref:`Variation`.
       - The location of the subject of the copy change.
    *  - copyChange
       -
-      - :ref:`MappableConcept`
+      - string
       - 1..1
-      - MUST use a `primaryCode` representing one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).
+      - MUST use one of the defined enumerations that are based on the corresponding EFO ontological terms for copy number variation. See Implementation Guidance for more details.

schema/vrs/json/Adjacency

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Adjacency",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/Adjacency",
    "title": "Adjacency",
    "type": "object",
    "maturity": "trial use",
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -69,7 +69,7 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceLocation"
                },
                {
                   "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
@@ -90,13 +90,13 @@
          "description": "The sequence found between adjoined sequences.",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/LengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/LengthExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/LiteralSequenceExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/ReferenceLengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/ReferenceLengthExpression"
             }
          ]
       },

schema/vrs/json/Allele

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Allele",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/Allele",
    "title": "Allele",
    "type": "object",
    "maturity": "trial use",
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -65,7 +65,7 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceLocation"
             },
             {
                "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
@@ -77,13 +77,13 @@
          "description": "An expression of the sequence state",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/LengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/LengthExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/LiteralSequenceExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/ReferenceLengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/ReferenceLengthExpression"
             }
          ]
       }

schema/vrs/json/CisPhasedBlock

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CisPhasedBlock",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/CisPhasedBlock",
    "title": "CisPhasedBlock",
    "type": "object",
    "maturity": "trial use",
@@ -52,7 +52,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -69,7 +69,7 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/Allele"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/Allele"
                },
                {
                   "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
@@ -79,7 +79,7 @@
          "description": "A list of Alleles that are found in-cis on a shared molecule."
       },
       "sequenceReference": {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceReference",
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceReference",
          "description": "An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles."
       }
    },

schema/vrs/json/CopyNumberChange

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CopyNumberChange",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/CopyNumberChange",
    "title": "CopyNumberChange",
    "type": "object",
    "maturity": "draft",
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -65,7 +65,7 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceLocation"
             },
             {
                "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
@@ -74,8 +74,18 @@
          "description": "The location of the subject of the copy change."
       },
       "copyChange": {
-         "description": "MUST use a `primaryCode` representing one of \"EFO:0030069\" (complete genomic loss), \"EFO:0020073\" (high-level loss), \"EFO:0030068\" (low-level loss), \"EFO:0030067\" (loss), \"EFO:0030064\" (regional base ploidy), \"EFO:0030070\" (gain), \"EFO:0030071\" (low-level gain), \"EFO:0030072\" (high-level gain).",
-         "$ref": "/ga4gh/schema/gks-core/1.0.0/json/MappableConcept"
+         "type": "string",
+         "enum": [
+            "complete genomic loss",
+            "high-level loss",
+            "low-level loss",
+            "loss",
+            "regional base ploidy",
+            "gain",
+            "low-level gain",
+            "high-level gain"
+         ],
+         "description": "MUST use one of the defined enumerations that are based on the corresponding EFO ontological terms for copy number variation. See Implementation Guidance for more details."
       }
    },
    "required": [

schema/vrs/json/CopyNumberCount

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/CopyNumberCount",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/CopyNumberCount",
    "title": "CopyNumberCount",
    "type": "object",
    "maturity": "trial use",
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -65,7 +65,7 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceLocation"
             },
             {
                "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"
@@ -76,7 +76,7 @@
       "copies": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/Range"
             },
             {
                "type": "integer"

schema/vrs/json/DerivativeMolecule

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/DerivativeMolecule",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/DerivativeMolecule",
    "title": "DerivativeMolecule",
    "type": "object",
    "maturity": "draft",
@@ -52,7 +52,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.1/json/Expression"
          }
       },
       "type": {
@@ -68,16 +68,16 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/Allele"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/Allele"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/CisPhasedBlock"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/CisPhasedBlock"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/Terminus"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/Terminus"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0/json/TraversalBlock"
+                  "$ref": "/ga4gh/schema/vrs/2.0.1/json/TraversalBlock"
                },
                {
                   "$ref": "/ga4gh/schema/gks-core/1.0.0/json/iriReference"

schema/vrs/json/Expression

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Expression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/Expression",
    "title": "Expression",
    "type": "object",
    "maturity": "trial use",

schema/vrs/json/LengthExpression

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/LengthExpression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/LengthExpression",
    "title": "LengthExpression",
    "type": "object",
    "maturity": "draft",
@@ -53,7 +53,7 @@
          "description": "The length of the sequence.",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/Range"
             },
             {
                "type": "integer"

schema/vrs/json/LiteralSequenceExpression

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/LiteralSequenceExpression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/LiteralSequenceExpression",
    "title": "LiteralSequenceExpression",
    "type": "object",
    "maturity": "trial use",
@@ -50,7 +50,7 @@
          "default": "LiteralSequenceExpression"
       },
       "sequence": {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/sequenceString",
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/sequenceString",
          "description": "the literal sequence"
       }
    },

schema/vrs/json/Location

@@ -1,13 +1,13 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Location",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/Location",
    "title": "Location",
    "type": "object",
    "maturity": "trial use",
    "description": "A contiguous segment of a biological sequence.",
    "oneOf": [
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/SequenceLocation"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/SequenceLocation"
       }
    ],
    "discriminator": {

schema/vrs/json/MolecularVariation

@@ -1,25 +1,25 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/MolecularVariation",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/MolecularVariation",
    "title": "MolecularVariation",
    "type": "object",
    "maturity": "trial use",
    "description": "A variation on a contiguous molecule.",
    "oneOf": [
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/Adjacency"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/Adjacency"
       },
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/Allele"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/Allele"
       },
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/CisPhasedBlock"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/CisPhasedBlock"
       },
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/DerivativeMolecule"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/DerivativeMolecule"
       },
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/Terminus"
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/Terminus"
       }
    ],
    "discriminator": {

schema/vrs/json/Range

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Range",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/Range",
    "title": "Range",
    "type": "array",
    "maturity": "trial use",

schema/vrs/json/ReferenceLengthExpression

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/ReferenceLengthExpression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.1/json/ReferenceLengthExpression",
    "title": "ReferenceLengthExpression",
    "type": "object",
    "maturity": "trial use",
@@ -53,7 +53,7 @@
       "length": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.1/json/Range"
             },
             {
                "type": "integer"
@@ -62,7 +62,7 @@
          "description": "The number of residues in the expressed sequence."
       },
       "sequence": {
-         "$ref": "/ga4gh/schema/vrs/2.0.0/json/sequenceString",
+         "$ref": "/ga4gh/schema/vrs/2.0.1/json/sequenceString",
          "description": "the literal Sequence encoded by the Reference Length Expression."
       },
       "repeatSubunitLength": {