From 3b3d9bee5fd8e8d4fc39c1b1f5aaf5604aecb9c3 Mon Sep 17 00:00:00 2001 From: Larry Babb Date: Thu, 7 Nov 2024 17:46:42 -0500 Subject: [PATCH] update SM & MSP to bring forward useful changes for all repos. (#72) --- .requirements.txt | 2 +- schema/cat-vrs/def/CanonicalAllele.rst | 7 ++-- schema/cat-vrs/def/CategoricalCnv.rst | 7 ++-- schema/cat-vrs/def/CategoricalVariant.rst | 32 ++++++++++++++++--- schema/cat-vrs/def/Constraint.rst | 9 +++--- schema/cat-vrs/def/CopyChangeConstraint.rst | 10 +++--- schema/cat-vrs/def/CopyCountConstraint.rst | 10 +++--- .../cat-vrs/def/DefiningAlleleConstraint.rst | 14 +++++--- .../def/DefiningLocationConstraint.rst | 15 ++++++--- .../def/ProteinSequenceConsequence.rst | 1 + submodules/vrs | 2 +- 11 files changed, 75 insertions(+), 34 deletions(-) diff --git a/.requirements.txt b/.requirements.txt index eda904f..8eeaa4a 100644 --- a/.requirements.txt +++ b/.requirements.txt @@ -2,6 +2,6 @@ pytest sphinx ~= 7.2 sphinx-rtd-theme ~= 1.2 pyyaml -ga4gh.gks.metaschema==0.3.0b14 +ga4gh.gks.metaschema==0.3.0b16 jsonschema referencing \ No newline at end of file diff --git a/schema/cat-vrs/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst index 6a91d2e..b9ef509 100644 --- a/schema/cat-vrs/def/CanonicalAllele.rst +++ b/schema/cat-vrs/def/CanonicalAllele.rst @@ -1,9 +1,7 @@ - .. warning:: This data class is at a **draft** maturity level and may change - significantly in future releases. Maturity levels are described in + significantly in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + **Computational Definition** A canonical allele is defined by an `Allele `_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations. @@ -18,6 +16,7 @@ A canonical allele is defined by an `Allele ⋮ - string - 0..m - Alternative name(s) for the Entity. * - extensions + - + .. raw:: html + + ⋮ - :ref:`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 + - - string - 1..1 - MUST be "CategoricalVariant" * - members + - + .. raw:: html + + ⋮ - :ref:`Variation` | :ref:`iriReference` - 0..m - A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant. * - constraints + - + .. raw:: html + + ⋮ - :ref:`Constraint` - 0..m - * - mappings + - + .. raw:: html + + ⋮ - :ref:`ConceptMapping` - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. diff --git a/schema/cat-vrs/def/Constraint.rst b/schema/cat-vrs/def/Constraint.rst index f332d1d..bd0accf 100644 --- a/schema/cat-vrs/def/Constraint.rst +++ b/schema/cat-vrs/def/Constraint.rst @@ -1,8 +1,7 @@ - .. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** Constraints are used to construct an intensional semantics of categorical variant types. @@ -17,10 +16,12 @@ Constraints are used to construct an intensional semantics of categorical varian :widths: auto * - Field + - Flags - Type - Limits - Description * - type + - - string - 1..1 - diff --git a/schema/cat-vrs/def/CopyChangeConstraint.rst b/schema/cat-vrs/def/CopyChangeConstraint.rst index f6a3097..be86265 100644 --- a/schema/cat-vrs/def/CopyChangeConstraint.rst +++ b/schema/cat-vrs/def/CopyChangeConstraint.rst @@ -1,8 +1,7 @@ - .. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** The relative assessment of the change in copies that members of this categorical variant satisfies. @@ -18,14 +17,17 @@ Some CopyChangeConstraint attributes are inherited from :ref:`Constraint`. :widths: auto * - Field + - Flags - Type - Limits - Description * - type + - - string - 1..1 - MUST be "CopyChangeConstraint" * - copyChange + - - string - 1..1 - The relative assessment of the change in copies that members of this categorical variant satisfies. diff --git a/schema/cat-vrs/def/CopyCountConstraint.rst b/schema/cat-vrs/def/CopyCountConstraint.rst index e052d01..33bf6c1 100644 --- a/schema/cat-vrs/def/CopyCountConstraint.rst +++ b/schema/cat-vrs/def/CopyCountConstraint.rst @@ -1,8 +1,7 @@ - .. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** The exact or range of copies that members of this categorical variant must satisfy. @@ -18,14 +17,17 @@ Some CopyCountConstraint attributes are inherited from :ref:`Constraint`. :widths: auto * - Field + - Flags - Type - Limits - Description * - type + - - string - 1..1 - MUST be "CopyCountConstraint" * - copies + - - integer | :ref:`Range` - 1..1 - The precise value or range of copies members of this categorical variant must satisfy. diff --git a/schema/cat-vrs/def/DefiningAlleleConstraint.rst b/schema/cat-vrs/def/DefiningAlleleConstraint.rst index 2aacbd4..2079afb 100644 --- a/schema/cat-vrs/def/DefiningAlleleConstraint.rst +++ b/schema/cat-vrs/def/DefiningAlleleConstraint.rst @@ -1,8 +1,7 @@ - .. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** The defining allele and its associated relationships that are congruent with member variants. @@ -18,18 +17,25 @@ Some DefiningAlleleConstraint attributes are inherited from :ref:`Constraint`. :widths: auto * - Field + - Flags - Type - Limits - Description * - type + - - string - 1..1 - MUST be "DefiningAlleleConstraint" * - allele + - - :ref:`Allele` | :ref:`iriReference` - 1..1 - * - relations + - + .. raw:: html + + ⋮ - string - 0..m - Defined relationships from which members relate to the defining allele. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. diff --git a/schema/cat-vrs/def/DefiningLocationConstraint.rst b/schema/cat-vrs/def/DefiningLocationConstraint.rst index d36e416..c834b79 100644 --- a/schema/cat-vrs/def/DefiningLocationConstraint.rst +++ b/schema/cat-vrs/def/DefiningLocationConstraint.rst @@ -1,8 +1,7 @@ - .. note:: This data class is at a **trial use** maturity level and may change - in future releases. Maturity levels are described in the :ref:`maturity-model`. - - + in future releases. Maturity levels are described in + the :ref:`maturity-model`. + **Computational Definition** The defining location and its associated relationships that are congruent with member locations. @@ -18,22 +17,30 @@ Some DefiningLocationConstraint attributes are inherited from :ref:`Constraint`. :widths: auto * - Field + - Flags - Type - Limits - Description * - type + - - string - 1..1 - MUST be "DefiningLocationConstraint" * - location + - - :ref:`SequenceLocation` | :ref:`iriReference` - 1..1 - * - relations + - + .. raw:: html + + ⋮ - string - 0..m - Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept. * - matchCharacteristic + - - string - 1..1 - A characteristic of the location that is used to match the defining location to member locations. diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst index ee435e1..0a4c435 100644 --- a/schema/cat-vrs/def/ProteinSequenceConsequence.rst +++ b/schema/cat-vrs/def/ProteinSequenceConsequence.rst @@ -12,6 +12,7 @@ A change that occurs in a protein sequence as a result of genomic changes. Due t :widths: auto * - Field + - Flags - Type - Limits - Description diff --git a/submodules/vrs b/submodules/vrs index 2aa22b0..8d533d6 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit 2aa22b0ade9a7823e6785bbcb5c2b8a6ee398ff8 +Subproject commit 8d533d623d55915f369b664a97f0319269a5e9d6