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ga4gh · Aug 12, 2024 · a7d7541 · a7d7541
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diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst
@@ -2,61 +2,61 @@
 
 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.
 
-    **Information Model**
-    
+**Information Model**
+
 Some Adjacency attributes are inherited from :ref:`Variation`.
 
-    .. list-table::
-       :class: clean-wrap
-       :header-rows: 1
-       :align: left
-       :widths: auto
-       
-       *  - Field
-          - Type
-          - Limits
-          - Description
-       *  - 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).
-       *  - label
-          - string
-          - 0..1
-          - A primary name for the entity.
-       *  - description
-          - string
-          - 0..1
-          - A free-text description of the entity.
-       *  - alternativeLabels
-          - string
-          - 0..m
-          - Alternative name(s) for the Entity.
-       *  - extensions
-          - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
-          - 0..m
-          - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
-       *  - expressions
-          - :ref:`Expression`
-          - 0..m
-          - 
-       *  - type
-          - string
-          - 1..1
-          - MUST be "Adjacency".
-       *  - adjoinedSequences
-          - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
-          - 2..2
-          - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
-       *  - linker
-          - :ref:`SequenceExpression`
-          - 0..1
-          - The sequence found between adjoined sequences.
-       *  - homology
-          - boolean
-          - 0..1
-          - A flag indicating if coordinate ambiguity in the adjoined sequences is from sequence homology (true) or other uncertainty (false).
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
+   *  - 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).
+   *  - label
+      - string
+      - 0..1
+      - A primary name for the entity.
+   *  - description
+      - string
+      - 0..1
+      - A free-text description of the entity.
+   *  - alternativeLabels
+      - string
+      - 0..m
+      - Alternative name(s) for the Entity.
+   *  - extensions
+      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - 0..m
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
+   *  - digest
+      - string
+      - 0..1
+      - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+   *  - expressions
+      - :ref:`Expression`
+      - 0..m
+      - 
+   *  - type
+      - string
+      - 1..1
+      - MUST be "Adjacency".
+   *  - adjoinedSequences
+      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - 2..2
+      - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
+   *  - linker
+      - :ref:`SequenceExpression`
+      - 0..1
+      - The sequence found between adjoined sequences.
+   *  - homology
+      - boolean
+      - 0..1
+      - A flag indicating if coordinate ambiguity in the adjoined sequences is from sequence homology (true) or other uncertainty, such as instrument ambiguity (false).
diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst
@@ -2,57 +2,57 @@
 
 The state of a molecule at a :ref:`Location`.
 
-    **Information Model**
-    
+**Information Model**
+
 Some Allele attributes are inherited from :ref:`Variation`.
 
-    .. list-table::
-       :class: clean-wrap
-       :header-rows: 1
-       :align: left
-       :widths: auto
-       
-       *  - Field
-          - Type
-          - Limits
-          - Description
-       *  - 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).
-       *  - label
-          - string
-          - 0..1
-          - A primary name for the entity.
-       *  - description
-          - string
-          - 0..1
-          - A free-text description of the entity.
-       *  - alternativeLabels
-          - string
-          - 0..m
-          - Alternative name(s) for the Entity.
-       *  - extensions
-          - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
-          - 0..m
-          - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
-       *  - expressions
-          - :ref:`Expression`
-          - 0..m
-          - 
-       *  - type
-          - string
-          - 1..1
-          - MUST be "Allele"
-       *  - location
-          - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
-          - 1..1
-          - The location of the Allele
-       *  - state
-          - :ref:`SequenceExpression`
-          - 1..1
-          - An expression of the sequence state
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
+   *  - 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).
+   *  - label
+      - string
+      - 0..1
+      - A primary name for the entity.
+   *  - description
+      - string
+      - 0..1
+      - A free-text description of the entity.
+   *  - alternativeLabels
+      - string
+      - 0..m
+      - Alternative name(s) for the Entity.
+   *  - extensions
+      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - 0..m
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
+   *  - digest
+      - string
+      - 0..1
+      - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+   *  - expressions
+      - :ref:`Expression`
+      - 0..m
+      - 
+   *  - type
+      - string
+      - 1..1
+      - MUST be "Allele"
+   *  - location
+      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - 1..1
+      - The location of the Allele
+   *  - state
+      - :ref:`SequenceExpression`
+      - 1..1
+      - An expression of the sequence state
diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst
@@ -2,57 +2,57 @@
 
 An ordered set of co-occurring :ref:`variants <Variation>` on the same molecule.
 
-    **Information Model**
-    
+**Information Model**
+
 Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
 
-    .. list-table::
-       :class: clean-wrap
-       :header-rows: 1
-       :align: left
-       :widths: auto
-       
-       *  - Field
-          - Type
-          - Limits
-          - Description
-       *  - 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).
-       *  - label
-          - string
-          - 0..1
-          - A primary name for the entity.
-       *  - description
-          - string
-          - 0..1
-          - A free-text description of the entity.
-       *  - alternativeLabels
-          - string
-          - 0..m
-          - Alternative name(s) for the Entity.
-       *  - extensions
-          - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
-          - 0..m
-          - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
-       *  - expressions
-          - :ref:`Expression`
-          - 0..m
-          - 
-       *  - type
-          - string
-          - 1..1
-          - MUST be "CisPhasedBlock"
-       *  - members
-          - :ref:`Allele` | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
-          - 2..m
-          - A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
-       *  - sequenceReference
-          - :ref:`SequenceReference`
-          - 0..1
-          - An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles.
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Type
+      - Limits
+      - Description
+   *  - 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).
+   *  - label
+      - string
+      - 0..1
+      - A primary name for the entity.
+   *  - description
+      - string
+      - 0..1
+      - A free-text description of the entity.
+   *  - alternativeLabels
+      - string
+      - 0..m
+      - Alternative name(s) for the Entity.
+   *  - extensions
+      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - 0..m
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
+   *  - digest
+      - string
+      - 0..1
+      - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+   *  - expressions
+      - :ref:`Expression`
+      - 0..m
+      - 
+   *  - type
+      - string
+      - 1..1
+      - MUST be "CisPhasedBlock"
+   *  - members
+      - :ref:`Allele` | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - 2..m
+      - A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
+   *  - sequenceReference
+      - :ref:`SequenceReference`
+      - 0..1
+      - An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles.