diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 1e552355..ec005df2 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,9 @@ build: tools: python: "3.11" +submodules: + include: all + sphinx: configuration: docs/source/conf.py diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst index d792643d..cce6a1d8 100644 --- a/schema/vrs/def/Adjacency.rst +++ b/schema/vrs/def/Adjacency.rst @@ -33,7 +33,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,7 +49,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`. - 1..1 - MUST be "Adjacency". * - adjoinedSequences - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 2..2 - The terminal sequence or pair of adjoined sequences that defines in the adjacency. * - linker diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst index 33082077..530268db 100644 --- a/schema/vrs/def/Allele.rst +++ b/schema/vrs/def/Allele.rst @@ -33,7 +33,7 @@ Some Allele attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,7 +49,7 @@ Some Allele attributes are inherited from :ref:`Variation`. - 1..1 - MUST be "Allele" * - location - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 1..1 - The location of the Allele * - state diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst index 04788f30..a30a549d 100644 --- a/schema/vrs/def/CisPhasedBlock.rst +++ b/schema/vrs/def/CisPhasedBlock.rst @@ -33,7 +33,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,7 +49,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`. - 1..1 - MUST be "CisPhasedBlock" * - members - - :ref:`Allele` | :ref:`IRI` + - :ref:`Allele` | `IRI `_ - 2..m - A list of :ref:`Alleles ` that are found in-cis on a shared molecule. * - sequenceReference diff --git a/schema/vrs/def/CopyNumber.rst b/schema/vrs/def/CopyNumber.rst index 4317010e..52052da3 100644 --- a/schema/vrs/def/CopyNumber.rst +++ b/schema/vrs/def/CopyNumber.rst @@ -37,7 +37,7 @@ Some CopyNumber attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,6 +49,6 @@ Some CopyNumber attributes are inherited from :ref:`Variation`. - 0..m - * - location - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 1..1 - A location for which the number of systemic copies is described. diff --git a/schema/vrs/def/CopyNumberChange.rst b/schema/vrs/def/CopyNumberChange.rst index 5a17f265..cb6c297f 100644 --- a/schema/vrs/def/CopyNumberChange.rst +++ b/schema/vrs/def/CopyNumberChange.rst @@ -33,7 +33,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -45,7 +45,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - 0..m - * - location - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 1..1 - A location for which the number of systemic copies is described. * - type @@ -53,6 +53,6 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - 1..1 - MUST be "CopyNumberChange" * - copyChange - - :ref:`Coding` + - `Coding <../data-types/data-types-source.json#/$defs/Coding>`_ - 1..1 - MUST be a `Coding` 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). diff --git a/schema/vrs/def/CopyNumberCount.rst b/schema/vrs/def/CopyNumberCount.rst index 073c986f..6e10fa32 100644 --- a/schema/vrs/def/CopyNumberCount.rst +++ b/schema/vrs/def/CopyNumberCount.rst @@ -33,7 +33,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -45,7 +45,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. - 0..m - * - location - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 1..1 - A location for which the number of systemic copies is described. * - type diff --git a/schema/vrs/def/DerivativeMolecule.rst b/schema/vrs/def/DerivativeMolecule.rst index 3754d1ab..e0de6ce0 100644 --- a/schema/vrs/def/DerivativeMolecule.rst +++ b/schema/vrs/def/DerivativeMolecule.rst @@ -33,7 +33,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,7 +49,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`. - 1..1 - MUST be "DerivativeMolecule". * - components - - :ref:`IRI` | :ref:`TraversalBlock` + - `IRI `_ | :ref:`TraversalBlock` - 2..m - The molecular components that constitute the derivative molecule. * - circular diff --git a/schema/vrs/def/Ga4ghIdentifiableObject.rst b/schema/vrs/def/Ga4ghIdentifiableObject.rst index efb09d1f..8e72b0f7 100644 --- a/schema/vrs/def/Ga4ghIdentifiableObject.rst +++ b/schema/vrs/def/Ga4ghIdentifiableObject.rst @@ -37,7 +37,7 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core-im:Ent - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 diff --git a/schema/vrs/def/LengthExpression.rst b/schema/vrs/def/LengthExpression.rst index 417f531a..88c1422b 100644 --- a/schema/vrs/def/LengthExpression.rst +++ b/schema/vrs/def/LengthExpression.rst @@ -33,7 +33,7 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/LiteralSequenceExpression.rst b/schema/vrs/def/LiteralSequenceExpression.rst index 165c33cf..edb18425 100644 --- a/schema/vrs/def/LiteralSequenceExpression.rst +++ b/schema/vrs/def/LiteralSequenceExpression.rst @@ -33,7 +33,7 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/ReferenceLengthExpression.rst b/schema/vrs/def/ReferenceLengthExpression.rst index e24f7452..01c167d9 100644 --- a/schema/vrs/def/ReferenceLengthExpression.rst +++ b/schema/vrs/def/ReferenceLengthExpression.rst @@ -33,7 +33,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/SequenceExpression.rst b/schema/vrs/def/SequenceExpression.rst index 4000ee5b..cbb0ff79 100644 --- a/schema/vrs/def/SequenceExpression.rst +++ b/schema/vrs/def/SequenceExpression.rst @@ -33,7 +33,7 @@ Some SequenceExpression attributes are inherited from :ref:`gks.core-im:Entity`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/SequenceLocation.rst b/schema/vrs/def/SequenceLocation.rst index 81cff67c..2ee65d2e 100644 --- a/schema/vrs/def/SequenceLocation.rst +++ b/schema/vrs/def/SequenceLocation.rst @@ -33,7 +33,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -45,7 +45,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec - 1..1 - MUST be "SequenceLocation" * - sequenceReference - - :ref:`IRI` | :ref:`SequenceReference` + - `IRI `_ | :ref:`SequenceReference` - 0..1 - A reference to a :ref:`Sequence` on which the location is defined. * - start diff --git a/schema/vrs/def/SequenceReference.rst b/schema/vrs/def/SequenceReference.rst index 70996bd4..dfb1d51b 100644 --- a/schema/vrs/def/SequenceReference.rst +++ b/schema/vrs/def/SequenceReference.rst @@ -33,7 +33,7 @@ Some SequenceReference attributes are inherited from :ref:`gks.core-im:Entity`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/Terminus.rst b/schema/vrs/def/Terminus.rst index 2d5b1966..85fac498 100644 --- a/schema/vrs/def/Terminus.rst +++ b/schema/vrs/def/Terminus.rst @@ -33,7 +33,7 @@ Some Terminus attributes are inherited from :ref:`Variation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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 @@ -49,6 +49,6 @@ Some Terminus attributes are inherited from :ref:`Variation`. - 1..1 - MUST be "Terminus". * - location - - :ref:`IRI` | :ref:`Location` + - `IRI `_ | :ref:`Location` - 1..1 - The location of the terminus. diff --git a/schema/vrs/def/TraversalBlock.rst b/schema/vrs/def/TraversalBlock.rst index cfc67172..874a81b9 100644 --- a/schema/vrs/def/TraversalBlock.rst +++ b/schema/vrs/def/TraversalBlock.rst @@ -33,7 +33,7 @@ Some TraversalBlock attributes are inherited from :ref:`gks.core-im:Entity`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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. * - type diff --git a/schema/vrs/def/Variation.rst b/schema/vrs/def/Variation.rst index b2e59fae..a5b6ea82 100644 --- a/schema/vrs/def/Variation.rst +++ b/schema/vrs/def/Variation.rst @@ -37,7 +37,7 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`. - 0..m - Alternative name(s) for the Entity. * - extensions - - :ref:`Extension` + - `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