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Added Example subsection to each class (using validation/models.yaml). #601

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Nov 26, 2024
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Added Example subsection to each class (using validation/models.yaml). #601

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18 changes: 18 additions & 0 deletions docs/source/concepts/LocationAndReference/SequenceLocation.rst
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Expand Up @@ -13,6 +13,24 @@ Definition and Information Model

.. include:: ../../def/vrs/SequenceLocation.rst

Example
@@@@@@@

The :ref:`SequenceLocation` for the position ``44908822`` is:

.. code-block:: json

{
"id": "ga4gh:SL.4t6JnYWqHwYw9WzBT_lmWBb3tLQNalkT",
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
},
"start": 44908821,
"end": 44908822
}

Implementation Guidance
@@@@@@@@@@@@@@@@@@@@@@@

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11 changes: 11 additions & 0 deletions docs/source/concepts/LocationAndReference/SequenceReference.rst
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Expand Up @@ -19,3 +19,14 @@ Definition and Information Model
################################

.. include:: ../../def/vrs/SequenceReference.rst

Example
#######

.. code-block:: json

{
"type": "SequenceReference",
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
"label": "NC_000007.14"
}
32 changes: 32 additions & 0 deletions docs/source/concepts/MolecularVariation/Adjacency.rst
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Expand Up @@ -17,6 +17,38 @@ Definition and Information Model

.. include:: ../../def/vrs/Adjacency.rst

Example
@@@@@@@

.. code-block:: json

{
"id": "ga4gh:AJ.O0IbSYyhnBAtUsR51bpdoqeSo4YaDMFo",
"type": "Adjacency",
"adjoinedSequences": [
{
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.9KdcA9ZpY1Cpvxvg8bMSLYDUpsX6GDLO",
"residueAlphabet": "na",
"id": "NC_000002.11"
},
"start": 456
},
{
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na",
"id": "NC_000001.10"
},
"end": 123
}
]
}

Implementation Guidance
@@@@@@@@@@@@@@@@@@@@@@@

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31 changes: 31 additions & 0 deletions docs/source/concepts/MolecularVariation/Allele.rst
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Expand Up @@ -12,6 +12,37 @@ Definition and Information Model

.. include:: ../../def/vrs/Allele.rst

Example
@@@@@@@

.. code-block:: json

{
"id": "ga4gh:VA.Oop4kjdTtKcg1kiZjIJAAR3bp7qi4aNT",
"type": "Allele",
"expressions": [
{
"syntax": "spdi",
"value": "NC_000001.11:40819438:CTCCTCCT:CTCCTCCTCCT"
}
],
"location": {
"type": "SequenceLocation",
"sequenceReference": {
"refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
"residueAlphabet": "na",
"id": "NC_000001.11"
},
"start": 40819438,
"end": 40819446
},
"state": {
"type": "ReferenceLengthExpression",
"length": 11,
"repeatSubunitLength": 3
}
}

Implementation Guidance
@@@@@@@@@@@@@@@@@@@@@@@

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42 changes: 42 additions & 0 deletions docs/source/concepts/MolecularVariation/CisPhasedBlock.rst
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Expand Up @@ -24,3 +24,45 @@ Definition and Information Model
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

.. include:: ../../def/vrs/CisPhasedBlock.rst

Example
@@@@@@@

.. code-block:: json

{
"id": "ga4gh:CPB.YAWwnFF0e-T7fnuT4wRzZW4Lzg7jc-zQ",
"type": "CisPhasedBlock",
"members": [
{
"location": {
"start": 601,
"end": 602,
"type": "SequenceLocation"
},
"state": {
"sequence": "C",
"type": "LiteralSequenceExpression"
},
"type": "Allele"
},
{
"location": {
"start": 701,
"end": 702,
"type": "SequenceLocation"
},
"state": {
"sequence": "C",
"type": "LiteralSequenceExpression"
},
"type": "Allele"
}
],
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na",
"id": "NC_000001.10"
}
}
70 changes: 69 additions & 1 deletion docs/source/concepts/MolecularVariation/DerivativeMolecule.rst
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Expand Up @@ -26,4 +26,72 @@ Traversal Block
The TraversalBlock is a key component of the `DerivativeMolecule` class, and is used for resolving the
orientation of double-stranded nucleic acid molecules when assembled into a derivative molecule.

.. include:: ../../def/vrs/TraversalBlock.rst
.. include:: ../../def/vrs/TraversalBlock.rst

Example
@@@@@@@

.. code-block:: json

{
"id": "ga4gh:DM.wthhP9ryLEU1ueo6V25gqbSVJC8H4z-M",
"type": "DerivativeMolecule",
"components": [
{
"type": "TraversalBlock",
"orientation": "forward",
"component": {
"type": "Adjacency",
"linker": {
"type": "LiteralSequenceExpression",
"sequence": "GTC"
},
"adjoinedSequences": [
{
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na",
"id": "NC_000001.10"
},
"end": 123
},
{
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.9KdcA9ZpY1Cpvxvg8bMSLYDUpsX6GDLO",
"residueAlphabet": "na",
"id": "NC_000002.11"
},
"start": 500
}
]
}
},
{
"type": "TraversalBlock",
"orientation": "forward",
"component": {
"type": "Adjacency",
"adjoinedSequences": [
{
"type": "SequenceLocation",
"end": 15000
},
{
"type": "SequenceLocation",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
"residueAlphabet": "na",
"id": "NC_000001.10"
},
"start": 10000
}
]
}
}
]
}
21 changes: 20 additions & 1 deletion docs/source/concepts/MolecularVariation/Terminus.rst
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Expand Up @@ -13,4 +13,23 @@ resulting from genomic rearrangements such as inversions or translocations.
Definition and Information Model
################################

.. include:: ../../def/vrs/Terminus.rst
.. include:: ../../def/vrs/Terminus.rst

Example
#######

.. code-block:: json

{
"id": "ga4gh:TM.8xpg7Q826fQJJ_6rImuqufhTXj0mh5gV",
"type": "Terminus"
"location": {
"end": 44908822,
"start": 44908821,
"sequenceReference": {
"refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
"type": "SequenceReference"
},
"type": "SequenceLocation"
}
}
10 changes: 10 additions & 0 deletions docs/source/concepts/SequenceExpression/LengthExpression.rst
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Expand Up @@ -13,3 +13,13 @@ Definition and Information Model
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

.. include:: ../../def/vrs/LengthExpression.rst

Example
@@@@@@@

.. code-block:: json

{
"type": "LengthExpression",
"length": 20000
}
10 changes: 10 additions & 0 deletions docs/source/concepts/SequenceExpression/LiteralSequenceExpression.rst
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Expand Up @@ -9,3 +9,13 @@ Definition and Information Model
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

.. include:: ../../def/vrs/LiteralSequenceExpression.rst

Example
@@@@@@@

.. code-block:: json

{
"sequence": "ACGT",
"type": "LiteralSequenceExpression"
}
12 changes: 12 additions & 0 deletions docs/source/concepts/SequenceExpression/ReferenceLengthExpression.rst
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Expand Up @@ -21,3 +21,15 @@ Definition and Information Model
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

.. include:: ../../def/vrs/ReferenceLengthExpression.rst

Example
@@@@@@@

.. code-block:: json

{
"type": "ReferenceLengthExpression",
"length": 11,
"repeatSubunitLength": 3,
"sequence": "CTCCTCCTCCT"
}
40 changes: 40 additions & 0 deletions docs/source/concepts/SystemicVariation/CopyNumber.rst
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Expand Up @@ -21,6 +21,26 @@ Definition and Information Model

.. _CopyNumberChange:

Example
#######

.. code-block:: json

{
"id": "ga4gh:CN.ezEUXykQvIhX8jHADILwC9f8k-jp8tZC",
"type": "CopyNumberCount",
"copies": [3, null],
"location": {
"sequenceReference": {
"refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
"type": "SequenceReference"
},
"end": 44909393,
"start": 44905795,
"type": "SequenceLocation"
}
}

Copy Number Change
@@@@@@@@@@@@@@@@

Expand All @@ -30,3 +50,23 @@ Definition and Information Model
################################

.. include:: ../../def/vrs/CopyNumberChange.rst

Example
#######

.. code-block:: json

{
"id": "ga4gh:CX.2_fT_6-IpUm5aS0wp8ZAkJ01MCE569L2",
"type": "CopyNumberChange",
"copyChange": "EFO:0030071",
"location": {
"sequenceReference": {
"refgetAccession": "SQ.jdEWLvLvT8827O59m1Agh5H3n6kTzBsJ",
"type": "SequenceReference"
},
"end": 44909393,
"start": 44905795,
"type": "SequenceLocation"
}
}
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