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@larrybabb
larrybabb committed Feb 10, 2025
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2 changes: 1 addition & 1 deletion docs/source/concepts/LocationAndReference/index.rst
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Expand Up @@ -15,4 +15,4 @@ and, by extension all references are built on, :ref:`Sequence References<Sequenc
:maxdepth: 1

SequenceLocation
SequenceReference
SequenceReference
2 changes: 1 addition & 1 deletion docs/source/concepts/SequenceExpression/LengthExpression.rst
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Expand Up @@ -6,7 +6,7 @@ Length Expression
.. admonition:: New in V2

The `LengthExpression` class is new in VRS v2, and was designed as a means for
handling unknown sequence content with known length.
handling unknown sequence content with known length.

A length expression is used to represent molecular sequences with known length
but unknown sequence content, typically as determined by molecular weight assays
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24 changes: 12 additions & 12 deletions schema/vrs/def/Adjacency.rst
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Expand Up @@ -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.
* - name
-
-
- string
- 0..1
- A primary name for the entity.
* - description
-
-
- string
- 0..1
- A free-text description of the Entity.
* - aliases
-
-
.. 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>
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22 changes: 11 additions & 11 deletions schema/vrs/def/Allele.rst
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Expand Up @@ -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.
* - name
-
-
- string
- 0..1
- A primary name for the entity.
* - description
-
-
- string
- 0..1
- A free-text description of the Entity.
* - aliases
-
-
.. 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
22 changes: 11 additions & 11 deletions schema/vrs/def/CisPhasedBlock.rst
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Expand Up @@ -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.
* - name
-
-
- string
- 0..1
- A primary name for the entity.
* - description
-
-
- string
- 0..1
- A free-text description of the Entity.
* - aliases
-
-
.. 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.
22 changes: 11 additions & 11 deletions schema/vrs/def/CopyNumberChange.rst
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Expand Up @@ -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.
* - name
-
-
- string
- 0..1
- A primary name for the entity.
* - description
-
-
- string
- 0..1
- A free-text description of the Entity.
* - aliases
-
-
.. 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).
22 changes: 11 additions & 11 deletions schema/vrs/def/CopyNumberCount.rst
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Expand Up @@ -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.
* - name
-
-
- string
- 0..1
- A primary name for the entity.
* - description
-
-
- string
- 0..1
- A free-text description of the Entity.
* - aliases
-
-
.. 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
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