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add ComposedSequenceExpressions #376

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Feb 9, 2022
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add ComposedSequenceExpressions #376

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b328c17
init ComposedSequenceExpression model
ahwagner Jan 27, 2022
331dcfe
set min items to 2 for components
ahwagner Jan 28, 2022
4c5d3a3
add docs
ahwagner Jan 28, 2022
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40 changes: 40 additions & 0 deletions docs/source/terms_and_model.rst
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Expand Up @@ -919,6 +919,46 @@ large-scale tandem duplications.
"type": "RepeatedSequenceExpression"
}

.. _ComposedSequenceExpression:

ComposedSequenceExpression
##########################

*Composed Sequence* is a class of sequence expression where two or more
constitutive sequence expressions are expressed as an ordered list,
representing a concatenated sequence. This class is useful for expressing
concepts such as the OPMD polyalanine alleles [2]_.

.. [2] Brais b, et al. *Short CCG expansions in the PABP2 gene cause
oculopharyngeal muscular dystrophy* Nat Genet. (1998).

.. include:: defs/ComposedSequenceExpression.rst

**Examples**

.. parsed-literal::

{
"type": "ComposedSequenceExpression",
"components": [
{
"type": "RepeatedSequenceExpression",
"seq_expr": { "type": "LiteralSequenceExpression", "sequence": "GCG" },
"count": { "type": "Number", "value": 11 }
},
{
"type": "RepeatedSequenceExpression",
"seq_expr": { "type": "LiteralSequenceExpression", "sequence": "GCA" },
"count": { "type": "Number", "value": 3 }
},
{
"type": "RepeatedSequenceExpression",
"seq_expr": { "type": "LiteralSequenceExpression", "sequence": "GCG" },
"count": { "type": "Number", "value": 1 }
}
]
}


.. _Feature:

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26 changes: 26 additions & 0 deletions schema/defs/vrs/ComposedSequenceExpression.rst
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@@ -0,0 +1,26 @@
**Computational Definition**

An expression of a sequence composed from multiple other :ref:`Sequence Expressions<SequenceExpression>` objects. MUST have at least one component that is not a ref:`LiteralSequenceExpression`. CANNOT be composed from nested composed sequence expressions.

**Information Model**

Some ComposedSequenceExpression attributes are inherited from :ref:`SequenceExpression`.

.. list-table::
:class: clean-wrap
:header-rows: 1
:align: left
:widths: auto

* - Field
- Type
- Limits
- Description
* - type
- string
- 1..1
- MUST be "ComposedSequenceExpression"
* - components
- :ref:`LiteralSequenceExpression` | :ref:`RepeatedSequenceExpression` | :ref:`DerivedSequenceExpression`
- 2..m
- An ordered list of :ref:`SequenceExpression` components comprising the expression.
33 changes: 33 additions & 0 deletions schema/vrs-source.yaml
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Expand Up @@ -460,6 +460,7 @@ definitions:
- $ref: "#/definitions/LiteralSequenceExpression"
- $ref: "#/definitions/DerivedSequenceExpression"
- $ref: "#/definitions/RepeatedSequenceExpression"
- $ref: "#/definitions/ComposedSequenceExpression"
discriminator:
propertyName: type
heritable_properties:
Expand Down Expand Up @@ -568,6 +569,38 @@ definitions:
minimum: 0
required: [ "seq_expr", "count" ]

ComposedSequenceExpression:
description: >-
An expression of a sequence composed from multiple other
:ref:`Sequence Expressions<SequenceExpression>`
objects. MUST have at least one component that is not a
ref:`LiteralSequenceExpression`. CANNOT be composed from
nested composed sequence expressions.
additionalProperties: false
type: object
properties:
type:
type: string
const: "ComposedSequenceExpression"
description: MUST be "ComposedSequenceExpression"
components:
type: array
uniqueItems: true
minItems: 2
items:
oneOf:
- $ref: "#/definitions/LiteralSequenceExpression"
- $ref: "#/definitions/RepeatedSequenceExpression"
- $ref: "#/definitions/DerivedSequenceExpression"
contains:
oneOf:
- $ref: "#/definitions/RepeatedSequenceExpression"
- $ref: "#/definitions/DerivedSequenceExpression"
description: >-
An ordered list of :ref:`SequenceExpression` components
comprising the expression.
required: [ "components" ]

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Feature

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48 changes: 48 additions & 0 deletions schema/vrs.json
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Expand Up @@ -618,6 +618,9 @@
},
{
"$ref": "#/definitions/RepeatedSequenceExpression"
},
{
"$ref": "#/definitions/ComposedSequenceExpression"
}
],
"discriminator": {
Expand Down Expand Up @@ -776,6 +779,51 @@
"type"
]
},
"ComposedSequenceExpression": {
"description": "An expression of a sequence composed from multiple other Sequence Expressions objects. MUST have at least one component that is not a ref:`LiteralSequenceExpression`. CANNOT be composed from nested composed sequence expressions.",
"additionalProperties": false,
"type": "object",
"properties": {
"type": {
"type": "string",
"const": "ComposedSequenceExpression",
"description": "MUST be \"ComposedSequenceExpression\""
},
"components": {
"type": "array",
"uniqueItems": true,
"minItems": 2,
"items": {
"oneOf": [
{
"$ref": "#/definitions/LiteralSequenceExpression"
},
{
"$ref": "#/definitions/RepeatedSequenceExpression"
},
{
"$ref": "#/definitions/DerivedSequenceExpression"
}
]
},
"contains": {
"oneOf": [
{
"$ref": "#/definitions/RepeatedSequenceExpression"
},
{
"$ref": "#/definitions/DerivedSequenceExpression"
}
]
},
"description": "An ordered list of SequenceExpression components comprising the expression."
}
},
"required": [
"components",
"type"
]
},
"Feature": {
"description": "A named entity that can be mapped to a Location. Genes, protein domains, exons, and chromosomes are some examples of common biological entities that may be Features.",
"oneOf": [
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30 changes: 30 additions & 0 deletions schema/vrs.yaml
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Expand Up @@ -373,6 +373,7 @@ definitions:
- $ref: '#/definitions/LiteralSequenceExpression'
- $ref: '#/definitions/DerivedSequenceExpression'
- $ref: '#/definitions/RepeatedSequenceExpression'
- $ref: '#/definitions/ComposedSequenceExpression'
discriminator:
propertyName: type
LiteralSequenceExpression:
Expand Down Expand Up @@ -471,6 +472,35 @@ definitions:
- count
- seq_expr
- type
ComposedSequenceExpression:
description: An expression of a sequence composed from multiple other Sequence
Expressions objects. MUST have at least one component that is not a ref:`LiteralSequenceExpression`.
CANNOT be composed from nested composed sequence expressions.
additionalProperties: false
type: object
properties:
type:
type: string
const: ComposedSequenceExpression
description: MUST be "ComposedSequenceExpression"
components:
type: array
uniqueItems: true
minItems: 2
items:
oneOf:
- $ref: '#/definitions/LiteralSequenceExpression'
- $ref: '#/definitions/RepeatedSequenceExpression'
- $ref: '#/definitions/DerivedSequenceExpression'
contains:
oneOf:
- $ref: '#/definitions/RepeatedSequenceExpression'
- $ref: '#/definitions/DerivedSequenceExpression'
description: An ordered list of SequenceExpression components comprising
the expression.
required:
- components
- type
Feature:
description: A named entity that can be mapped to a Location. Genes, protein domains,
exons, and chromosomes are some examples of common biological entities that
Expand Down