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| .. warning:: This data class is at a **draft** maturity level and may \ | ||
| change significantly in future releases. Maturity \ | ||
| levels are described in the :ref:`maturity-model`. | ||
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| **Computational Definition** | ||
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| 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. | ||
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| **GA4GH Digest** | ||
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| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
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| * - Prefix | ||
| - Keys | ||
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| * - AJ | ||
| - ['adjoinedSequences', 'linker', 'type'] | ||
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| **Information Model** | ||
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| Some Adjacency attributes are inherited from :ref:`Variation`. | ||
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| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
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| * - Field | ||
| - Flags | ||
| - 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 label for the entity. | ||
| * - description | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - A free-text description of the entity. | ||
| * - extensions | ||
| - | ||
| .. raw:: html | ||
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| <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">↓</span> | ||
| - :ref:`Extension` | ||
| - 0..m | ||
| - | ||
| * - type | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - MUST be "Adjacency". | ||
| * - digest | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - A sha512t24u digest created using the VRS Computed Identifier algorithm. | ||
| * - expressions | ||
| - | ||
| .. raw:: html | ||
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| <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">⋮</span> | ||
| - :ref:`Expression` | ||
| - 0..m | ||
| - | ||
| * - adjoinedSequences | ||
| - | ||
| .. raw:: html | ||
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| <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">↓</span> | ||
| - :ref:`IRI` | :ref:`Location` | ||
| - 1..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. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| .. warning:: This data class is at a **draft** maturity level and may \ | ||
| change significantly in future releases. Maturity \ | ||
| levels are described in the :ref:`maturity-model`. | ||
|
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| **Computational Definition** | ||
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| The state of a molecule at a :ref:`Location`. | ||
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| **GA4GH Digest** | ||
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| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
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| * - Prefix | ||
| - Keys | ||
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| * - VA | ||
| - ['location', 'state', 'type'] | ||
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| **Information Model** | ||
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| Some Allele attributes are inherited from :ref:`Variation`. | ||
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| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
|
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| * - Field | ||
| - Flags | ||
| - 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 label for the entity. | ||
| * - description | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - A free-text description of the entity. | ||
| * - extensions | ||
| - | ||
| .. raw:: html | ||
|
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| <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">↓</span> | ||
| - :ref:`Extension` | ||
| - 0..m | ||
| - | ||
| * - type | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - MUST be "Allele" | ||
| * - digest | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - A sha512t24u digest created using the VRS Computed Identifier algorithm. | ||
| * - expressions | ||
| - | ||
| .. raw:: html | ||
|
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| <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">⋮</span> | ||
| - :ref:`Expression` | ||
| - 0..m | ||
| - | ||
| * - location | ||
| - | ||
| - :ref:`IRI` | :ref:`Location` | ||
| - 1..1 | ||
| - The location of the Allele | ||
| * - state | ||
| - | ||
| - :ref:`SequenceExpression` | ||
| - 1..1 | ||
| - An expression of the sequence state |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| .. warning:: This data class is at a **draft** maturity level and may \ | ||
| change significantly in future releases. Maturity \ | ||
| levels are described in the :ref:`maturity-model`. | ||
|
|
||
| **Computational Definition** | ||
|
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| An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell, etc.) relative to a baseline ploidy. | ||
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| **GA4GH Digest** | ||
|
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||
| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
|
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| * - Prefix | ||
| - Keys | ||
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| * - CX | ||
| - ['copyChange', 'location', 'type'] | ||
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| **Information Model** | ||
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| Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. | ||
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| .. list-table:: | ||
| :class: clean-wrap | ||
| :header-rows: 1 | ||
| :align: left | ||
| :widths: auto | ||
|
|
||
| * - Field | ||
| - Flags | ||
| - 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 label for the entity. | ||
| * - description | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - A free-text description of 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="Ordered">↓</span> | ||
| - :ref:`Extension` | ||
| - 0..m | ||
| - | ||
| * - type | ||
| - | ||
| - string | ||
| - 0..1 | ||
| - MUST be "CopyNumberChange" | ||
| * - 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">⋮</span> | ||
| - :ref:`Expression` | ||
| - 0..m | ||
| - | ||
| * - location | ||
| - | ||
| - :ref:`IRI` | :ref:`Location` | ||
| - 1..1 | ||
| - A location for which the number of systemic copies is described. | ||
| * - copyChange | ||
| - | ||
| - string | ||
| - 1..1 | ||
| - MUST be 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). |
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