re-run with new msp v3.1

Author: larrybabb

schema/vrs/def/Adjacency.rst

@@ -37,69 +37,69 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
-      -
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
-      -
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - digest
-      -
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
-      -
+      - 
    *  - type
-      -
+      - 
       - string
       - 1..1
       - MUST be "Adjacency".
    *  - adjoinedSequences
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Ordered">&#8595;</span>
       - :ref:`iriReference` | :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
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>

schema/vrs/def/Allele.rst

@@ -37,61 +37,61 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
-      -
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
-      -
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - digest
-      -
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
-      -
+      - 
    *  - type
-      -
+      - 
       - string
       - 1..1
       - MUST be "Allele"
    *  - location
-      -
+      - 
       - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the Allele
    *  - state
-      -
+      - 
       - :ref:`SequenceExpression`
       - 1..1
       - An expression of the sequence state

schema/vrs/def/CisPhasedBlock.rst

@@ -37,64 +37,64 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
-      -
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
-      -
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - digest
-      -
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
-      -
+      - 
    *  - type
-      -
+      - 
       - string
       - 1..1
       - MUST be "CisPhasedBlock"
    *  - members
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Allele` | :ref:`iriReference`
       - 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.

schema/vrs/def/CopyNumberChange.rst

@@ -37,61 +37,61 @@ Some CopyNumberChange attributes are inherited from :ref:`Variation`.
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
-      -
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
-      -
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - digest
-      -
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
-      -
+      - 
    *  - type
-      -
+      - 
       - string
       - 1..1
       - MUST be "CopyNumberChange"
    *  - location
-      -
+      - 
       - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the subject of the copy change.
    *  - copyChange
-      -
+      - 
       - :ref:`MappableConcept`
       - 1..1
       - MUST use a `primaryCode` representing one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).

schema/vrs/def/CopyNumberCount.rst

@@ -37,61 +37,61 @@ Some CopyNumberCount attributes are inherited from :ref:`Variation`.
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
-      -
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
-      -
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - digest
-      -
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
-      -
+      - 
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
-      -
+      - 
    *  - type
-      -
+      - 
       - string
       - 1..1
       - MUST be "CopyNumberCount"
    *  - location
-      -
+      - 
       - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the subject of the copy count.
    *  - copies
-      -
+      - 
       - integer | :ref:`Range`
       - 1..1
       - The integral number of copies of the subject in a system