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update model to passing
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@ahwagner
ahwagner committed Nov 7, 2023
1 parent 9bcc0e9 commit 65c9f1b
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Showing 9 changed files with 277 additions and 46 deletions.
4 changes: 2 additions & 2 deletions examples/simple_breakpoint.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ breakends:
location:
type: SequenceLocation
sequenceReference:
refgetAccession: 7aI9u0vheriv13er
refgetAccession: SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
residueAlphabet: na
id: NC_000001.10
start: 123
Expand All @@ -15,7 +15,7 @@ breakends:
location:
type: SequenceLocation
sequenceReference:
refgetAccession: hiu2gii33iv13er
refgetAccession: SQ.9KdcA9ZpY1Cpvxvg8bMSLYDUpsX6GDLO
residueAlphabet: na
id: NC_000002.11
start: 456
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2 changes: 1 addition & 1 deletion schema/defs/vrs/Breakend.rst
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Expand Up @@ -19,7 +19,7 @@ A break in a molecule with respect to a reference sequence indicating the sequen
- 1..1
- MUST be "Breakend"
* - location
- Location
- :ref:`Location` | `IRI <core.json#/$defs/IRI>`_
- 1..1
- The interval over which the break could occur in
* - orientation
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32 changes: 27 additions & 5 deletions schema/defs/vrs/Breakpoint.rst
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Expand Up @@ -4,6 +4,8 @@ A rearrangement resulting in sequences flanking the two breakends becoming adjac

**Information Model**

Some Breakpoint attributes are inherited from :ref:`ValueObject`.

.. list-table::
:class: clean-wrap
:header-rows: 1
Expand All @@ -14,26 +16,46 @@ A rearrangement resulting in sequences flanking the two breakends becoming adjac
- 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
- `Extension <core.json#/$defs/Extension>`_
- 0..m
-
* - digest
- string
- 0..1
- A sha512t24u digest created using the VRS Computed Identifier algorithm.
* - type
- string
- 1..1
- MUST be "Breakpoint"
* - breakends
- Breakend
- `IRI <core.json#/$defs/IRI>`_ | :ref:`Breakend`
- 1..2
- Breakends involed in the sequence
- Breakends involved in the sequence
* - insertion
- DefiniteRange
- :ref:`Range`
- 0..1
- Approximate length of unknown sequence between the breaks.
* - homology
- boolean
- 0..1
- A flag indicating whether the location interval of the breakend is due to the sequences at the breakends being homologous or whether the interval is due to uncertainty regarding the actual locations of the breakends.
* - sequence
- LiteralSequenceExpression
- `IRI <core.json#/$defs/IRI>`_ | :ref:`SequenceExpression`
- 0..1
- Sequence occuring after the break.
- Sequence occurring after the break.
* - terminal
- boolean
- 0..1
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2 changes: 1 addition & 1 deletion schema/defs/vrs/SequenceReference.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ Some SequenceReference attributes are inherited from :ref:`ValueObject`.
- A sha512t24u digest created using the VRS Computed Identifier algorithm.
* - type
- string
- 1..1
- 0..1
-
* - refgetAccession
- string
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76 changes: 68 additions & 8 deletions schema/merged.json
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Original file line number Diff line number Diff line change
Expand Up @@ -624,8 +624,7 @@
}
},
"required": [
"refgetAccession",
"type"
"refgetAccession"
],
"additionalProperties": false
},
Expand Down Expand Up @@ -860,6 +859,13 @@
},
"Breakend": {
"maturity": "Alpha",
"ga4ghDigest": {
"keys": [
"type",
"location",
"orientation"
]
},
"description": "A break in a molecule with respect to a reference sequence indicating the sequence deviates from the reference sequence after or before this location.",
"type": "object",
"properties": {
Expand All @@ -870,7 +876,14 @@
"description": "MUST be \"Breakend\""
},
"location": {
"type": "Location",
"oneOf": [
{
"$ref": "#/$defs/IRI"
},
{
"$ref": "#/$defs/SequenceLocation"
}
],
"description": "The interval over which the break could occur in"
},
"orientation": {
Expand All @@ -891,9 +904,39 @@
},
"Breakpoint": {
"maturity": "Alpha",
"ga4ghDigest": {
"keys": [
"type",
"breakends"
]
},
"description": "A rearrangement resulting in sequences flanking the two breakends becoming adjacent sequences on the same molecule.",
"type": "object",
"properties": {
"id": {
"type": "string",
"description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)."
},
"label": {
"type": "string",
"description": "A primary label for the entity."
},
"description": {
"type": "string",
"description": "A free-text description of the entity."
},
"extensions": {
"type": "array",
"ordered": true,
"items": {
"$ref": "#/$defs/Extension"
}
},
"digest": {
"description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.",
"type": "string",
"pattern": "[0-9A-Za-z_\\-]{32}"
},
"type": {
"type": "string",
"const": "Breakpoint",
Expand All @@ -905,14 +948,21 @@
"uniqueItems": false,
"ordered": false,
"items": {
"type": "Breakend"
"oneOf": [
{
"$ref": "#/$defs/Breakend"
},
{
"$ref": "#/$defs/IRI"
}
]
},
"description": "Breakends involed in the sequence",
"description": "Breakends involved in the sequence",
"minItems": 1,
"maxItems": 2
},
"insertion": {
"type": "DefiniteRange",
"$ref": "#/$defs/Range",
"description": "Approximate length of unknown sequence between the breaks."
},
"homology": {
Expand All @@ -921,8 +971,18 @@
"description": "A flag indicating whether the location interval of the breakend is due to the sequences at the breakends being homologous or whether the interval is due to uncertainty regarding the actual locations of the breakends."
},
"sequence": {
"type": "LiteralSequenceExpression",
"description": "Sequence occuring after the break."
"oneOf": [
{
"$ref": "#/$defs/IRI"
},
{
"$ref": "#/$defs/LiteralSequenceExpression"
},
{
"$ref": "#/$defs/ReferenceLengthExpression"
}
],
"description": "Sequence occurring after the break."
},
"terminal": {
"type": "boolean",
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51 changes: 44 additions & 7 deletions schema/merged.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -480,7 +480,6 @@ $defs:
- na
required:
- refgetAccession
- type
additionalProperties: false
SequenceExpression:
description: An expression describing a Sequence.
Expand Down Expand Up @@ -659,6 +658,11 @@ $defs:
pattern: ^[A-Z*\-]*$
Breakend:
maturity: Alpha
ga4ghDigest:
keys:
- type
- location
- orientation
description: A break in a molecule with respect to a reference sequence indicating
the sequence deviates from the reference sequence after or before this location.
type: object
Expand All @@ -669,7 +673,9 @@ $defs:
default: Breakend
description: MUST be "Breakend"
location:
type: Location
oneOf:
- $ref: '#/$defs/IRI'
- $ref: '#/$defs/SequenceLocation'
description: The interval over which the break could occur in
orientation:
type: string
Expand All @@ -686,10 +692,36 @@ $defs:
additionalProperties: false
Breakpoint:
maturity: Alpha
ga4ghDigest:
keys:
- type
- breakends
description: A rearrangement resulting in sequences flanking the two breakends
becoming adjacent sequences on the same molecule.
type: object
properties:
id:
type: string
description: 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:
type: string
description: A primary label for the entity.
description:
type: string
description: A free-text description of the entity.
extensions:
type: array
ordered: true
items:
$ref: '#/$defs/Extension'
digest:
description: A sha512t24u digest created using the VRS Computed Identifier
algorithm.
type: string
pattern: '[0-9A-Za-z_\-]{32}'
type:
type: string
const: Breakpoint
Expand All @@ -700,12 +732,14 @@ $defs:
uniqueItems: false
ordered: false
items:
type: Breakend
description: Breakends involed in the sequence
oneOf:
- $ref: '#/$defs/Breakend'
- $ref: '#/$defs/IRI'
description: Breakends involved in the sequence
minItems: 1
maxItems: 2
insertion:
type: DefiniteRange
$ref: '#/$defs/Range'
description: Approximate length of unknown sequence between the breaks.
homology:
type: boolean
Expand All @@ -714,8 +748,11 @@ $defs:
is due to the sequences at the breakends being homologous or whether the
interval is due to uncertainty regarding the actual locations of the breakends.
sequence:
type: LiteralSequenceExpression
description: Sequence occuring after the break.
oneOf:
- $ref: '#/$defs/IRI'
- $ref: '#/$defs/LiteralSequenceExpression'
- $ref: '#/$defs/ReferenceLengthExpression'
description: Sequence occurring after the break.
terminal:
type: boolean
default: false
Expand Down
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