fixed/updated some rst references/issues for new vrs 2.x xref

docs/source/appendices/index.rst

@@ -2,47 +2,16 @@ Appendices
 !!!!!!!!!!
 
 
-blah
+.. TODO:: Either add general landing page material for all appendices here or include the content of the different subsections directly.
 
 
 .. toctree::
    :maxdepth: 2
 
    design_decisions
-   development_process
-   future_plans
-
-   implementations
-   relationships
-   associating_annotations
-   equivalence
-   ga4gh_identifiers
-   truncated_digest_collision_analysis
-
    faq
    glossary
 
 
-.. .. toctree::
-    :maxdepth: 2
-    design_decisions
-    glossary
-    relationships
-    faq
-
-
-
-
-..    truncated_digest_collision_analysis
-..    future_plans
-..    implementations
-    equivalence
-    associating_annotations
-    ga4gh_identifiers
-    development_process
-    
-
-
-
 
 

docs/source/def

@@ -0,0 +1 @@
+../../schema/catvrs/def

docs/source/releases/1.0.rst → docs/source/releases/index.rst

@@ -1,5 +1,7 @@
-1.0
-!!!
+.. `Releases`:
+
+1.0 (pre-releases)
+!!!!!!!!!!!!!!!!!!
 
 1.0.0.04-2024.connect
 @@@@@@@@@@@@@@@@@@@@@

docs/source/rst_epilog

@@ -10,6 +10,8 @@
 .. _VRS Gene: https://vrs.ga4gh.org/en/latest/terms_and_model.html#gene
 
 .. |vrs| replace:: `VRS <https://vrs.ga4gh.org/>`__
+.. |vrs_yaml| replace:: `VRS YAML <https://github.com/ga4gh/vrs/tree/2.x/schema/vrs/vrs-source.yaml>`__
+.. |vrs_json| replace:: `VRS JSON <https://github.com/ga4gh/vrs/tree/2.x/schema/vrs/json>`__
 
 .. |eg| replace:: *e.g.,*
 .. |ie| replace:: *i.e.,*

docs/source/schema.rst

@@ -13,14 +13,14 @@ Machine Readable Specifications
 The machine readable Cat-VRS is written using `JSON Schema
 <https://json-schema.org/>`_.
 
-The schema itself is written in YAML (|vrs_yaml|) and converted to JSON
-(|vrs_json|).
+The schema itself is written in YAML (|vrs_yaml|) and converted to individual
+JSON files for each class in the schema (|vrs_json|).
 
 Contributions to the schema MUST be written in the YAML document.
 
 
 .. _CategoricalVariationSchemata:
-
+.. _CategoricalVariation:
 
 Categorical Variation Schemata
 @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@@ -33,32 +33,32 @@ PLEASE CHECK BACK IN THE FUTURE!
     :alt: An irresistably cute kittynaut beckoning you to enter the Cat-VRS.
     :align: center
 
-.. include:: defs/CategoricalVariation.rst
+.. include:: def/CategoricalVariation.rst
 
-.. _Canonical:
+.. _CanonicalAllele:
 
 Canonical Allele
 ################
 
-.. include:: defs/CanonicalAllele.rst
+.. include:: def/CanonicalAllele.rst
 
-.. _Described:
+.. _DescribedVariation:
 
 Described Variation
 ###################
 
-.. include:: defs/DescribedVariation.rst
+.. include:: def/DescribedVariation.rst
 
-.. _CatCNV:
+.. _CategoricalCnv:
 
 Categorical Copy Number
 #######################
 
-.. include:: defs/CategoricalCnv.rst
+.. include:: def/CategoricalCnv.rst
 
-.. _ProtConsequence:
+.. _ProteinSequenceConsequence:
 
 Protein Sequence Consequence
 ############################
 
-.. include:: defs/ProteinSequenceConsequence.rst
+.. include:: def/ProteinSequenceConsequence.rst

schema/catvrs/catvrs-source.yaml

@@ -13,7 +13,7 @@ namespaces:
   gks.common: ../gks-common/common.yaml#/$defs/
 
 $defs:
-  # VRSATILE Categorical Variation are presented top-down. Everything rolls up to
+  # Categorical Variation are presented top-down. Everything rolls up to
   # CategoricalVariation, which is a polymorphic abstraction of many kinds of
   # categorical variation.
 

schema/catvrs/def/CanonicalAllele.rst

@@ -19,7 +19,7 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
        *  - id
           - string
           - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
        *  - label
           - string
           - 0..1
@@ -29,11 +29,11 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
           - 0..1
           - A free-text description of the entity.
        *  - extensions
-          - `Extension <../gks-common/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - mappings
-          - `Mapping <../gks-common/core.json#/$defs/Mapping>`_
+          - `Mapping <../gks-common/common.json#/$defs/Mapping>`_
           - 0..m
           - 
        *  - type
@@ -45,10 +45,10 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
           - 0..m
           - Aliases are alternate labels for a Domain Entity.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with variants on alternate reference sequences.

schema/catvrs/def/CategoricalCnv.rst

@@ -19,7 +19,7 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
        *  - id
           - string
           - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
        *  - label
           - string
           - 0..1
@@ -29,11 +29,11 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
           - 0..1
           - A free-text description of the entity.
        *  - extensions
-          - `Extension <../gks-common/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - mappings
-          - `Mapping <../gks-common/core.json#/$defs/Mapping>`_
+          - `Mapping <../gks-common/common.json#/$defs/Mapping>`_
           - 0..m
           - 
        *  - type
@@ -45,7 +45,7 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
           - 0..m
           - Aliases are alternate labels for a Domain Entity.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - location

schema/catvrs/def/CategoricalVariation.rst

@@ -4,7 +4,7 @@ A representation of a categorically-defined domain for variation, in which indiv
 
     **Information Model**
 
-Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEntity`.
+Some CategoricalVariation attributes are inherited from :ref:`gks.common:DomainEntity`.
 
     .. list-table::
        :class: clean-wrap
@@ -19,7 +19,7 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt
        *  - id
           - string
           - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
        *  - label
           - string
           - 0..1
@@ -29,11 +29,11 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt
           - 0..1
           - A free-text description of the entity.
        *  - extensions
-          - `Extension <../gks-common/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - mappings
-          - `Mapping <../gks-common/core.json#/$defs/Mapping>`_
+          - `Mapping <../gks-common/common.json#/$defs/Mapping>`_
           - 0..m
           - 
        *  - type
@@ -45,6 +45,6 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt
           - 0..m
           - Aliases are alternate labels for a Domain Entity.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.

schema/catvrs/def/DescribedVariation.rst

@@ -19,13 +19,13 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
        *  - id
           - string
           - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
        *  - extensions
-          - `Extension <../gks-common/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - mappings
-          - `Mapping <../gks-common/core.json#/$defs/Mapping>`_
+          - `Mapping <../gks-common/common.json#/$defs/Mapping>`_
           - 0..m
           - 
        *  - type
@@ -37,7 +37,7 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
           - 0..m
           - Aliases are alternate labels for a Domain Entity.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - label

schema/catvrs/def/ProteinSequenceConsequence.rst

@@ -19,7 +19,7 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
        *  - id
           - string
           - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
        *  - label
           - string
           - 0..1
@@ -29,11 +29,11 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
           - 0..1
           - A free-text description of the entity.
        *  - extensions
-          - `Extension <../gks-common/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - mappings
-          - `Mapping <../gks-common/core.json#/$defs/Mapping>`_
+          - `Mapping <../gks-common/common.json#/$defs/Mapping>`_
           - 0..m
           - 
        *  - type
@@ -45,10 +45,10 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
           - 0..m
           - Aliases are alternate labels for a Domain Entity.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/core.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with (projects to the same codons) as alleles on other protein reference  sequences.