Merge branch 'issue-565' into 2.x

schema/vrs/vrs-source.yaml

@@ -27,6 +27,7 @@ $defs:
   # =============================================================================
 
   Ga4ghIdentifiableObject:
+    maturity: trial use
     inherits: gks.core-im:Entity
     description: >-
       An object for which a GA4GH computed identifier can be created.
@@ -42,6 +43,7 @@ $defs:
         pattern: '^[0-9A-Za-z_\-]{32}$'
 
   Variation:
+    maturity: trial use
     inherits: Ga4ghIdentifiableObject
     description: >-
       A representation of the state of one or more biomolecules.
@@ -59,7 +61,7 @@ $defs:
 
   Expression:
     type: object
-    maturity: draft
+    maturity: trial use
     # protectedClassOf: Variation
     description: >-
       Representation of a variation by a specified nomenclature or syntax for a Variation object.
@@ -119,7 +121,7 @@ $defs:
   # Molecular Variation
 
   Allele:
-    maturity: draft
+    maturity: trial use
     ga4ghDigest:
       prefix: VA
       keys:
@@ -149,7 +151,7 @@ $defs:
     required: [ "location", "state" ]
 
   CisPhasedBlock:
-    maturity: draft
+    maturity: trial use
     ga4ghDigest:
       prefix: CPB
       keys:
@@ -189,6 +191,7 @@ $defs:
   # SystemicVariation
 
   CopyNumber:
+    maturity: draft
     ga4ghDigest:
       keys:
         - location
@@ -268,7 +271,7 @@ $defs:
       propertyName: type
 
   SequenceLocation:
-    maturity: draft
+    maturity: trial use
     ga4ghDigest:
       keys:
         - start
@@ -312,7 +315,7 @@ $defs:
         $ref: "#/$defs/SequenceString"
 
   SequenceReference:
-    maturity: draft
+    maturity: trial use
     inherits: gks.core-im:Entity
     ga4ghDigest:
       keys:
@@ -355,6 +358,7 @@ $defs:
   # SequenceExpression
 
   SequenceExpression:
+    maturity: trial use
     inherits: gks.core-im:Entity
     ga4ghDigest:
       keys:
@@ -376,7 +380,7 @@ $defs:
       - type
 
   ReferenceLengthExpression:
-    maturity: draft
+    maturity: trial use
     inherits: SequenceExpression
     ga4ghDigest:
       keys:
@@ -428,7 +432,7 @@ $defs:
           - type: integer
 
   LiteralSequenceExpression:
-    maturity: draft
+    maturity: trial use
     inherits: SequenceExpression
     ga4ghDigest:
       keys:
@@ -451,7 +455,7 @@ $defs:
   # Numerics, Comparators, and Ranges
 
   Range:
-    maturity: draft
+    maturity: trial use
     description: An inclusive range of values bounded by one or more integers.
     type: array
     ordered: true
@@ -463,7 +467,7 @@ $defs:
     minItems: 2
 
   Residue:
-    maturity: draft
+    maturity: trial use
     description: >-
       A character representing a specific residue (i.e., molecular species)
       or groupings of these ("ambiguity codes"), using `one-letter IUPAC
@@ -473,7 +477,7 @@ $defs:
     pattern: '[A-Z*\-]'
 
   SequenceString:
-    maturity: draft
+    maturity: trial use
     description: >-
       A character string of :ref:`Residues <Residue>` that represents a biological
       sequence using the conventional sequence order (5’-to-3’ for
@@ -490,17 +494,17 @@ $defs:
   # =============================================================================
 
   Adjacency:
-    maturity: draft
+    maturity: trial use
     ga4ghDigest:
       prefix: AJ
       keys:
         - adjoinedSequences
         - linker
     inherits: MolecularVariation
     description: >-
-      The `Adjacency` class can represent either the termination of a sequence
-      or the adjoining of the end of a sequence with the beginning of an
-      adjacent sequence, potentially with an intervening linker sequence.
+      The `Adjacency` class represents the adjoining of the end of a sequence with
+      the beginning of an adjacent sequence, potentially with an intervening linker
+      sequence.
     type: object
     properties:
       type: