* primitive styling change

* update gks-core sm

docs/source/concepts/AdditionalDataTypes/Code.rst

@@ -1,6 +1,6 @@
-.. _Code:
+.. _code:
 
-Code
+code
 !!!!
 
-.. include::  ../../def/gks-core/Code.rst
+.. include::  ../../def/gks-core/code.rst

docs/source/concepts/AdditionalDataTypes/index.rst

@@ -69,19 +69,19 @@ Range
 
 .. include:: ../../def/vrs/Range.rst
 
-.. _Residue:
+.. _residue:
 
-Residue
+residue
 #######
 
-.. include:: ../../def/vrs/Residue.rst
+.. include:: ../../def/vrs/residue.rst
 
-.. _SequenceString:
+.. _sequenceString:
 
-SequenceString
+sequenceString
 ##############
 
-.. include:: ../../def/vrs/SequenceString.rst
+.. include:: ../../def/vrs/sequenceString.rst
 
 Imported Classes
 @@@@@@@@@@@@@@@@
@@ -96,5 +96,5 @@ Work Stream as common data classes.
    Element
    Extension
    Coding
-   Code
-   IRI
+   code
+   iriReference

docs/source/concepts/AdditionalDataTypes/iriReference.rst

@@ -0,0 +1,6 @@
+.. _iriReference:
+
+iriReference
+!!!!!!!!!!!!
+
+.. include::  ../../def/gks-core/iriReference.rst

schema/vrs/def/Adjacency.rst

@@ -54,7 +54,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Adjacency".
    *  - adjoinedSequences
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 2..2
       - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
    *  - linker

schema/vrs/def/Allele.rst

@@ -54,7 +54,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Allele"
    *  - location
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the Allele
    *  - state

schema/vrs/def/CisPhasedBlock.rst

@@ -54,7 +54,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "CisPhasedBlock"
    *  - members
-      - :ref:`Allele` | :ref:`IRI`
+      - :ref:`Allele` | :ref:`iriReference`
       - 2..m
       - A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
    *  - sequenceReference

schema/vrs/def/CopyNumber.rst

@@ -55,6 +55,6 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - location
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.

schema/vrs/def/CopyNumberChange.rst

@@ -51,7 +51,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - type

schema/vrs/def/CopyNumberCount.rst

@@ -51,7 +51,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - type

schema/vrs/def/DerivativeMolecule.rst

@@ -55,7 +55,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "DerivativeMolecule".
    *  - components
-      - :ref:`IRI` | :ref:`Allele` | :ref:`CisPhasedBlock` | :ref:`Terminus` | :ref:`TraversalBlock`
+      - :ref:`iriReference` | :ref:`Allele` | :ref:`CisPhasedBlock` | :ref:`Terminus` | :ref:`TraversalBlock`
       - 2..m
       - The molecular components that constitute the derivative molecule.
    *  - circular

schema/vrs/def/LiteralSequenceExpression.rst

@@ -46,6 +46,6 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
       - 1..1
       - MUST be "LiteralSequenceExpression"
    *  - sequence
-      - :ref:`SequenceString`
+      - :ref:`sequenceString`
       - 1..1
       - the literal sequence

schema/vrs/def/ReferenceLengthExpression.rst

@@ -50,7 +50,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
       - 1..1
       - The number of residues in the expressed sequence.
    *  - sequence
-      - :ref:`SequenceString`
+      - :ref:`sequenceString`
       - 0..1
       - the literal :ref:`Sequence` encoded by the Reference Length Expression.
    *  - repeatSubunitLength

schema/vrs/def/SequenceLocation.rst

@@ -50,7 +50,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 1..1
       - MUST be "SequenceLocation"
    *  - sequenceReference
-      - :ref:`IRI` | :ref:`SequenceReference`
+      - :ref:`iriReference` | :ref:`SequenceReference`
       - 0..1
       - A reference to a :ref:`Sequence` on which the location is defined.
    *  - start
@@ -62,6 +62,6 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 0..1
       - The end coordinate or range of the SequenceLocation. The minimum value of this coordinate or range is 0. MUST represent a coordinate or range greater than or equal to the value of `start`.
    *  - sequence
-      - :ref:`SequenceString`
+      - :ref:`sequenceString`
       - 0..1
       - The literal sequence encoded by the `sequenceReference` at these coordinates.

schema/vrs/def/SequenceString.rst

@@ -5,4 +5,4 @@
 
 **Computational Definition**
 
-A character string of :ref:`Residues <Residue>` that represents a biological sequence using the conventional sequence order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.
+A character string of :ref:`residues <residue>` that represents a biological sequence using the conventional sequence order (5’-to-3’ for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.

schema/vrs/def/Terminus.rst

@@ -55,6 +55,6 @@ Some Terminus attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Terminus".
    *  - location
-      - :ref:`IRI` | :ref:`Location`
+      - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the terminus.

schema/vrs/json/Adjacency

@@ -72,7 +72,7 @@
                   "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
                }
             ],
             "not": {

schema/vrs/json/Allele

@@ -68,7 +68,7 @@
                "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
          "description": "The location of the Allele"

schema/vrs/json/CisPhasedBlock

@@ -72,7 +72,7 @@
                   "$ref": "/ga4gh/schema/vrs/2.x/json/Allele"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
                }
             ]
          },

schema/vrs/json/CopyNumberChange

@@ -62,7 +62,7 @@
                "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
          "description": "A location for which the number of systemic copies is described."

schema/vrs/json/CopyNumberCount

@@ -62,7 +62,7 @@
                "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
          "description": "A location for which the number of systemic copies is described."

schema/vrs/json/DerivativeMolecule

@@ -80,7 +80,7 @@
                   "$ref": "/ga4gh/schema/vrs/2.x/json/TraversalBlock"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
                }
             ]
          },

schema/vrs/json/LiteralSequenceExpression

@@ -50,7 +50,7 @@
          "default": "LiteralSequenceExpression"
       },
       "sequence": {
-         "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceString",
+         "$ref": "/ga4gh/schema/vrs/2.x/json/sequenceString",
          "description": "the literal sequence"
       }
    },

schema/vrs/json/ReferenceLengthExpression

@@ -62,7 +62,7 @@
          "description": "The number of residues in the expressed sequence."
       },
       "sequence": {
-         "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceString",
+         "$ref": "/ga4gh/schema/vrs/2.x/json/sequenceString",
          "description": "the literal Sequence encoded by the Reference Length Expression."
       },
       "repeatSubunitLength": {

schema/vrs/json/Residue

@@ -1,7 +1,7 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Residue",
-   "title": "Residue",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/residue",
+   "title": "residue",
    "type": "string",
    "maturity": "trial use",
    "description": "A character representing a specific residue (i.e., molecular species) or groupings of these (\"ambiguity codes\"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.",

schema/vrs/json/SequenceLocation

@@ -62,7 +62,7 @@
                "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceReference"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
          "description": "A reference to a Sequence on which the location is defined."
@@ -91,7 +91,7 @@
       },
       "sequence": {
          "description": "The literal sequence encoded by the `sequenceReference` at these coordinates.",
-         "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceString"
+         "$ref": "/ga4gh/schema/vrs/2.x/json/sequenceString"
       }
    },
    "required": [

schema/vrs/json/SequenceString

@@ -1,9 +1,9 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/SequenceString",
-   "title": "SequenceString",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/sequenceString",
+   "title": "sequenceString",
    "type": "string",
    "maturity": "trial use",
-   "description": "A character string of Residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.",
+   "description": "A character string of residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.",
    "pattern": "^[A-Z*\\-]*$"
 }

schema/vrs/json/Terminus

@@ -67,7 +67,7 @@
                "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
          "description": "The location of the terminus."