some images and doc updates

ga4gh · Dec 4, 2023 · fa5e5f3 · fa5e5f3
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diff --git a/docs/source/datatypes_classes/base_types.rst b/docs/source/datatypes_classes/base_types.rst
@@ -1,14 +1,29 @@
-VRS Type Framework
-@@@@@@@@@@@@@@@@@@
+VRS Base Types
+@@@@@@@@@@@@@@
 
-The VRS Type Framework is a set of classes that can be used to create 
+The VRS Base Types are a set of classes that can be used to create 
 VRS data classes that can be used to represent variation and location
-data. It uses core elements of the GKS Common Framework as a foundation.
+data. It uses core elements of the GKS Common as a foundation.
 
-    entity
-    value_object
+.. _Entity:
 
+.. include:: ../defs/gks.common/Entity.rst
 
+Entity
+######
+
+.. _ValueObject:
+
+ValueObject
+###########
+
+.. include:: ../defs/vrs/ValueObject.rst
+
+Ga4ghIdentifiableObject
+#######################
+
+.. include:: ../defs/vrs/Ga4ghIdentifiableObject.rst
+
 .. _Location:
 
 Location
@@ -24,7 +39,7 @@ The most common and concrete Location is a :ref:`SequenceLocation`, i.e.,
 a Location based on a named sequence and an Interval on that sequence. Other 
 types of Location may be added based on community need.
 
-.. include:: defs/Location.rst
+.. include:: ../defs/vrs/Location.rst
 
 **Implementation Guidance**
 
@@ -52,20 +67,24 @@ subclass <utilityvariation>`. Types of variation are widely varied, and
 there are several :ref:`planned-variation` currently under consideration
 to capture this diversity.
 
-.. include:: defs/Variation.rst
+.. include:: ../defs/vrs/Variation.rst
 
 .. _MolecularVariation:
 
 Molecular Variation
 $$$$$$$$$$$$$$$$$$$
 
-.. include:: defs/MolecularVariation.rst
+.. include:: ../defs/vrs/MolecularVariation.rst
 
 .. _SystemicVariation:
 
 Systemic Variation
 $$$$$$$$$$$$$$$$$$
 
-.. include:: defs/SystemicVariation.rst
+.. include:: ../defs/vrs/SystemicVariation.rst
+
 
+CopyNumber
+##########
 
+.. include:: ../defs/vrs/CopyNumber.rst
diff --git a/docs/source/datatypes_classes/classes.rst b/docs/source/datatypes_classes/classes.rst
@@ -9,7 +9,7 @@ $$$$$$$$$$$$$$$$
 A *Sequence Location* is a specified subsequence of a reference :ref:`Sequence`.
 The reference is typically a chromosome, transcript, or protein sequence.
 
-.. include:: ../defs/SequenceLocation.rst
+.. include::  ../defs/vrs/SequenceLocation.rst
 
 **Implementation Guidance**
 
@@ -64,7 +64,7 @@ genetic locus. In the genetics community, *allele* may also refer to a
 specific haplotype. In the context of biological sequences, "allele" refers
 to a distinct state of a molecule at a location.
 
-.. include:: ../defs/Allele.rst
+.. include::  ../defs/vrs/Allele.rst
 
 **Implementation Guidance**
 
@@ -178,7 +178,7 @@ on the same physical molecule. Haplotypes are commonly described with respect
 to locations on a gene, a set of nearby genes, or other physically proximal
 genetic markers that tend to be transmitted together.
 
-.. include:: ../defs/Haplotype.rst
+.. include::  ../defs/vrs/Haplotype.rst
 
 **Implementation Guidance**
 
@@ -300,7 +300,7 @@ of :ref:`SystemicVariation` and so describes the number of copies in a
 genome. The related :ref:`MolecularVariation` concept can be expressed
 as an :ref:`Allele` with a :ref:`RepeatedSequenceExpression`.
 
-.. include:: ../defs/CopyNumberCount.rst
+.. include::  ../defs/vrs/CopyNumberCount.rst
 
 **Examples**
 
@@ -335,7 +335,7 @@ callers typically express changes as relative statements, and many HGVS
 expressions submitted to express copy number variation are interpreted to be
 relative copy changes.
 
-.. include:: ../defs/CopyNumberChange.rst
+.. include::  ../defs/vrs/CopyNumberChange.rst
 
 **Examples**
 
@@ -363,7 +363,7 @@ to either by individual nucleotide representations (e.g. GT representation in VC
 genotypes using either :ref:`Allele` objects (as commonly done in VCF records) or larger :ref:`Haplotype`
 objects (which would otherwise be represented using symbolic shorthand).
 
-.. include:: ../defs/Genotype.rst
+.. include::  ../defs/vrs/Genotype.rst
 
 **Implementation guidance**
 

diff --git a/docs/source/datatypes_classes/general_purpose.rst b/docs/source/datatypes_classes/general_purpose.rst
@@ -3,8 +3,37 @@ General Purpose Types
 
 TBD describe and pull the gks-common general puprose datatypes used by vrs
 
+Range
+#####
 
-    range
-    expression
-    coding
-    mappable
+.. include:: ../defs/vrs/Range.rst
+
+Expression
+##########
+
+.. include:: ../defs/vrs/Expression.rst
+
+Code
+####
+
+.. include:: ../defs/gks.common/Code.rst
+
+Coding
+######
+
+.. include:: ../defs/gks.common/Coding.rst
+
+Mapping
+#######
+
+.. include:: ../defs/gks.common/Mapping.rst
+
+MappableEntity
+##############
+
+.. include:: ../defs/gks.common/MappableEntity.rst
+
+Extension
+#########
+
+.. include:: ../defs/gks.common/Extension.rst
diff --git a/docs/source/datatypes_classes/primitives.rst b/docs/source/datatypes_classes/primitives.rst
@@ -4,58 +4,12 @@ Primitive Types
 Primitive types represent simple values with syntactic or other
 constraints. They enable correctness for values stored in VRS.
 
-.. _CURIE:
+.. _IRI:
 
-CURIE
-#####
+IRI
+###
 
-.. include:: ../defs/CURIE.rst
-
-**Implementation Guidance**
-
-* All identifiers in VRS MUST be a valid CURIE, regardless of
-  whether the identifier refers to GA4GH VRS objects or external data.
-* For GA4GH VRS objects, this specification RECOMMENDS using globally
-  unique :ref:`computed-identifiers` for use within *and* between
-  systems.
-* For external data, CURIE-formatted identifiers MUST be used.  When
-  an appropriate namespace exists at `identifiers.org
-  <http://identifiers.org/>`__, that namespace MUST be used.  When an
-  appropriate namespace does not exist at `identifiers.org
-  <http://identifiers.org/>`__, support is implementation-dependent.
-  That is, implementations MAY choose whether and how to support
-  informal or local namespaces.
-* Implementations MUST use CURIE identifiers verbatim. Implementations
-  MAY NOT modify CURIEs in any way (e.g., case-folding).
-
-**Examples**
-
-Identifiers for GRCh38 chromosome 19:
-
-.. parsed-literal::
-
-    ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
-    refseq:NC_000019.10
-    grch38:19
-
-See :ref:`identify` for examples of CURIE-based identifiers for VRS
-objects.
-
-
-**Information Model**
-
-A string constrained to match the regular expression
-``^cen|[pq](ter|([1-9][0-9]*(\.[1-9][0-9]*)?))$``, derived from the
-ISCN guidelines [1]_.
-
-.. [1] McGowan-Jordan J (Ed.). *ISCN 2016: An international system
-       for human cytogenomic nomenclature (2016).* Karger (2016).
-
-**Examples**
-
-.. parsed-literal::
-
-   "q13.32" (string)
+.. include::  ../defs/vrs/IRI.rst
 
 .. _Residue:
 
@@ -66,19 +20,19 @@ A residue refers to a specific `monomer`_ within the `polymeric
 chain`_ of a `protein`_ or `nucleic acid`_ (Source: `Wikipedia
 Residue page`_).
 
-.. include:: ../defs/Residue.rst
+.. include::  ../defs/vrs/Residue.rst
 
-.. _Sequence:
+.. _SequenceString:
 
-Sequence
-########
+SequenceString
+##############
 
 A *sequence* is a character string representation of a contiguous,
 linear polymer of nucleic acid or amino acid :ref:`Residues <Residue>`.
 Sequences are the prevalent representation of these polymers,
 particularly in the domain of variant representation.
 
-.. include:: ../defs/Sequence.rst
+.. include::  ../defs/vrs/SequenceString.rst
 
 **Information Model**
 

diff --git a/docs/source/datatypes_classes/special_purpose.rst b/docs/source/datatypes_classes/special_purpose.rst
@@ -18,7 +18,7 @@ sequence, but are intended to be semantically distinct. There MAY be
 reasons to select or enforce one form over another that SHOULD be
 managed by implementations. See discussion on :ref:`equivalence`.
 
-.. include:: ../defs/SequenceExpression.rst
+.. include::  ../defs/vrs/SequenceExpression.rst
 
 .. _ReferenceLengthExpression:
 
@@ -27,7 +27,7 @@ ReferenceLengthExpression
 
 A ReferenceLengthExpression ...
 
-.. include:: ../defs/ReferenceLengthExpression.rst
+.. include::  ../defs/vrs/ReferenceLengthExpression.rst
 
 **Examples**
 
@@ -42,7 +42,7 @@ LengthExpression
 
 A LengthExpression ...
 
-.. include:: ../defs/LengthExpression.rst
+.. include::  ../defs/vrs/LengthExpression.rst
 
 **Examples**
 
@@ -58,7 +58,7 @@ LiteralSequenceExpression
 A LiteralSequenceExpression "wraps" a string representation of a
 sequence for parallelism with other SequenceExpressions.
 
-.. include:: ../defs/LiteralSequenceExpression.rst
+.. include::  ../defs/vrs/LiteralSequenceExpression.rst
 
 **Examples**
 
@@ -77,11 +77,11 @@ Sequence Reference
 
 tbd
 
-.. include:: ../defs/SequenceReference.rst
+.. include::  ../defs/vrs/SequenceReference.rst
 
 .. _genotypemember:
 
 GenotypeMember
 @@@@@@@@@@@@@@
 
-.. include:: ../defs/GenotypeMember.rst
+.. include::  ../defs/vrs/GenotypeMember.rst
diff --git a/docs/source/defs b/docs/source/defs
@@ -1 +1 @@
-../../schema/defs/vrs
+../../schema/defs
diff --git a/docs/source/images/branch_management.png b/docs/source/images/branch_management.png
diff --git a/docs/source/images/maturity_levels.png b/docs/source/images/maturity_levels.png