Release log and ga4gh.inherent (#604)

* add 2.0 release notes * update ga4gh inherent convention (closes #598)
ga4gh · Nov 26, 2024 · 0106b48 · 0106b48
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diff --git a/.requirements.txt b/.requirements.txt
@@ -3,7 +3,7 @@ jsonschema
 referencing
 ipython
 pyyaml
-ga4gh.gks.metaschema==0.3.0b17
+ga4gh.gks.metaschema==0.3.0
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 jupyterlab

diff --git a/docs/source/appendices/ga4gh_identifiers.rst b/docs/source/appendices/ga4gh_identifiers.rst
@@ -69,9 +69,9 @@ reference:
 
 GA4GH Digest Keys
 #################
-When creating computed identifiers from objects, VRS uses a custom schema
-attribute, *ga4ghDigest*, that contains the keys used for filtering out
-properties. For example, the Allele JSON Schema:
+When creating computed identifiers from objects, VRS uses a custom schema attribute, 
+*ga4gh.inherent*, that contains the property names used for computing digests. For example, 
+the Allele JSON Schema:
 
 .. parsed-literal::
 
@@ -81,9 +81,9 @@ properties. For example, the Allele JSON Schema:
    "title": "Allele",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "VA",
-      "keys": [
+      "inherent": [
          "location",
          "state",
          "type"
@@ -95,9 +95,8 @@ properties. For example, the Allele JSON Schema:
 
 .. note::
 
-  The `ga4ghDigest` property names are currently being aligned with the Sequence
-  Collections effort (see `SeqCol#84 <https://github.com/ga4gh/refget/issues/84>`_)
-  and may potentially change.
+  The `ga4gh` JSON Schema namespace is aligned with the Sequence Collections effort 
+  (see `SeqCol#84 <https://github.com/ga4gh/refget/issues/84>`_).
 
 GA4GH Type Prefixes
 @@@@@@@@@@@@@@@@@@@
@@ -122,4 +121,4 @@ We use the following guidelines for type prefixes:
 Administration
 ##############
 
-Type prefix administration is to be managed by the `GA4GH TASC`_.
+Type prefixes, pURL registration, and JSON Schema keyword administration are coordinated with the `GA4GH TASC`_.
diff --git a/docs/source/releases/2.0.rst b/docs/source/releases/2.0.rst
@@ -0,0 +1,16 @@
+2.0
+!!!
+
+2.0.0
+@@@@@
+
+Major Changes
+#############
+
+  * implements the :ref:`_maturity-model` for all data classes
+  * classes now support descriptive metadata
+  * digests now rely on inherent property descriptions
+  * object references now use IRI references instead of CURIEs
+  * supports structural variation
+  * imports from the GKS-core library for cross-specification alignment
+  * renames Haplotype to CisPhasedBlock
diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst
@@ -15,7 +15,7 @@ The `Adjacency` class represents the adjoining of the end of a sequence with the
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - AJ
        - ['adjoinedSequences', 'linker', 'type']

diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst
@@ -15,7 +15,7 @@ The state of a molecule at a :ref:`Location`.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - VA
        - ['location', 'state', 'type']

diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst
@@ -15,7 +15,7 @@ An ordered set of co-occurring :ref:`variants <Variation>` on the same molecule.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - CPB
        - ['members', 'type']

diff --git a/schema/vrs/def/CopyNumberChange.rst b/schema/vrs/def/CopyNumberChange.rst
@@ -15,7 +15,7 @@ An assessment of the copy number of a :ref:`Location` within a system (e.g. geno
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - CX
        - ['copyChange', 'location', 'type']

diff --git a/schema/vrs/def/CopyNumberCount.rst b/schema/vrs/def/CopyNumberCount.rst
@@ -15,7 +15,7 @@ The absolute count of discrete copies of a :ref:`Location` within a system (e.g.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - CN
        - ['copies', 'location', 'type']

diff --git a/schema/vrs/def/DerivativeMolecule.rst b/schema/vrs/def/DerivativeMolecule.rst
@@ -15,7 +15,7 @@ A molecule derived from segments of multiple adjoined molecular sequences, typic
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - DM
        - ['components', 'type']

diff --git a/schema/vrs/def/Ga4ghIdentifiableObject.rst b/schema/vrs/def/Ga4ghIdentifiableObject.rst
@@ -15,7 +15,7 @@ An object for which a GA4GH computed identifier can be created.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['type']

diff --git a/schema/vrs/def/LengthExpression.rst b/schema/vrs/def/LengthExpression.rst
@@ -15,7 +15,7 @@ A sequence expressed only by its length.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['length', 'type']

diff --git a/schema/vrs/def/LiteralSequenceExpression.rst b/schema/vrs/def/LiteralSequenceExpression.rst
@@ -15,7 +15,7 @@ An explicit expression of a Sequence.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['sequence', 'type']

diff --git a/schema/vrs/def/ReferenceLengthExpression.rst b/schema/vrs/def/ReferenceLengthExpression.rst
@@ -15,7 +15,7 @@ An expression of a sequence that is derived from repeating a subsequence of an a
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['length', 'repeatSubunitLength', 'type']

diff --git a/schema/vrs/def/SequenceExpression.rst b/schema/vrs/def/SequenceExpression.rst
@@ -15,7 +15,7 @@ An expression describing a :ref:`Sequence`.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['type']

diff --git a/schema/vrs/def/SequenceLocation.rst b/schema/vrs/def/SequenceLocation.rst
@@ -15,7 +15,7 @@ A :ref:`Location` defined by an interval on a referenced :ref:`Sequence`.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - SL
        - ['end', 'sequenceReference', 'start', 'type']

diff --git a/schema/vrs/def/SequenceReference.rst b/schema/vrs/def/SequenceReference.rst
@@ -15,7 +15,7 @@ A sequence of nucleic or amino acid character codes.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['refgetAccession', 'type']

diff --git a/schema/vrs/def/Terminus.rst b/schema/vrs/def/Terminus.rst
@@ -15,7 +15,7 @@ The `Terminus` data class provides a structure for describing the end (terminus)
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - TM
        - ['location', 'type']

diff --git a/schema/vrs/def/TraversalBlock.rst b/schema/vrs/def/TraversalBlock.rst
@@ -15,7 +15,7 @@ A component used to describe the orientation of applicable molecular variation w
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['type', 'component', 'orientation']

diff --git a/schema/vrs/def/Variation.rst b/schema/vrs/def/Variation.rst
@@ -15,7 +15,7 @@ A representation of the state of one or more biomolecules.
     :widths: auto
 
     *  - Prefix
-       - Keys
+       - Inherent
 
     *  - None
        - ['type']

diff --git a/schema/vrs/json/Adjacency b/schema/vrs/json/Adjacency
@@ -4,9 +4,9 @@
    "title": "Adjacency",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "AJ",
-      "keys": [
+      "inherent": [
          "adjoinedSequences",
          "linker",
          "type"

diff --git a/schema/vrs/json/Allele b/schema/vrs/json/Allele
@@ -4,9 +4,9 @@
    "title": "Allele",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "VA",
-      "keys": [
+      "inherent": [
          "location",
          "state",
          "type"

diff --git a/schema/vrs/json/CisPhasedBlock b/schema/vrs/json/CisPhasedBlock
@@ -4,9 +4,9 @@
    "title": "CisPhasedBlock",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "CPB",
-      "keys": [
+      "inherent": [
          "members",
          "type"
       ]

diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange
@@ -4,8 +4,8 @@
    "title": "CopyNumberChange",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "copyChange",
          "location",
          "type"

diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount
@@ -4,8 +4,8 @@
    "title": "CopyNumberCount",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "copies",
          "location",
          "type"

diff --git a/schema/vrs/json/DerivativeMolecule b/schema/vrs/json/DerivativeMolecule
@@ -4,9 +4,9 @@
    "title": "DerivativeMolecule",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "DM",
-      "keys": [
+      "inherent": [
          "components",
          "type"
       ]

diff --git a/schema/vrs/json/LengthExpression b/schema/vrs/json/LengthExpression
@@ -4,8 +4,8 @@
    "title": "LengthExpression",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "length",
          "type"
       ]

diff --git a/schema/vrs/json/LiteralSequenceExpression b/schema/vrs/json/LiteralSequenceExpression
@@ -4,8 +4,8 @@
    "title": "LiteralSequenceExpression",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "sequence",
          "type"
       ]

diff --git a/schema/vrs/json/ReferenceLengthExpression b/schema/vrs/json/ReferenceLengthExpression
@@ -4,8 +4,8 @@
    "title": "ReferenceLengthExpression",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "length",
          "repeatSubunitLength",
          "type"

diff --git a/schema/vrs/json/SequenceLocation b/schema/vrs/json/SequenceLocation
@@ -4,8 +4,8 @@
    "title": "SequenceLocation",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "end",
          "sequenceReference",
          "start",

diff --git a/schema/vrs/json/SequenceReference b/schema/vrs/json/SequenceReference
@@ -4,8 +4,8 @@
    "title": "SequenceReference",
    "type": "object",
    "maturity": "trial use",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "refgetAccession",
          "type"
       ]

diff --git a/schema/vrs/json/Terminus b/schema/vrs/json/Terminus
@@ -4,9 +4,9 @@
    "title": "Terminus",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
+   "ga4gh": {
       "prefix": "TM",
-      "keys": [
+      "inherent": [
          "location",
          "type"
       ]

diff --git a/schema/vrs/json/TraversalBlock b/schema/vrs/json/TraversalBlock
@@ -4,8 +4,8 @@
    "title": "TraversalBlock",
    "type": "object",
    "maturity": "draft",
-   "ga4ghDigest": {
-      "keys": [
+   "ga4gh": {
+      "inherent": [
          "type",
          "component",
          "orientation"