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Issue 191: Align readthedocs with VRS and VA-Spec style of one concept per page (#195)
* Initial refactor * Added Categorical Variant class to Data Model index * Hid table of contents from homepage, like VRS does * Added line break in the data model page * Moved Constraint to concepts root * Added Adjacency and Gene Fusion * Removed raw html elements * Removed duplicate entries in imported/index, subclasses automatically shown * Removed extra exclaimations
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‎docs/source/concepts/CategoricalVariant.rst‎

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.. _CategoricalVariant:
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Categorical Variant
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!!!!!!!!!!!!!!!!!!!
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The Categorical Variant class is the primary class in Cat-VRS. It
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depends on one or more :ref:`Constraint <constraints>` elements to create a complete
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description of a categorical variant.
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.. include:: ../def/cat-vrs/CategoricalVariant.rst

‎docs/source/concepts/Constraint.rst‎

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.. _constraint:
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Constraint
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!!!!!!!!!!
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The *Constraint* class is an abstract class that is the parent of all other :ref:`Constraint classes <constraints>`. A constraint is a rule or set of rules that a variant must satisfy to qualify as a valid member of the :ref:`Categorical Variant <CategoricalVariant>`. Constraint subclasses are only used in Categorical Variant objects.
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.. include:: ../def/cat-vrs/Constraint.rst

‎docs/source/concepts/Constraints/AdjacencyConstraint.rst‎

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.. _AdjacencyConstraint:
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Adjacency Constraint
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!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/AdjacencyConstraint.rst
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Examples
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The following are example implementations of AdjacencyConstraint:
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.. collapse:: BCR(ncbi:613)::ABL1(ncbi:25)
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_adjacencyFusion-ex1
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:language: json
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:lines: 42-75
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.. collapse:: v::NTRK1(hgnc:8031)
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_adjacencyFusion-ex2
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:language: json
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:lines: 15-37
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.. collapse:: ?::ZNF384(ncbi:171017)
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_adjacencyFusion-ex3
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:language: json
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:lines: 15-37
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.. collapse:: FGFR2(hgnc:3689)::v
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_adjacencyFusion-ex4
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:language: json
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:lines: 15-88
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Implementation Guidance
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The Adjacency Constraint is similar to `VRS' Adjacency class <https://vrs.ga4gh.org/en/stable/concepts/MolecularVariation/Adjacency.html>`_, except that the `adjoinedElements` field supports data types in addition to :ref:`iriReference` and :ref:`Location`.
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We recommend following the `Variant Interpretation for Cancer Consortium's Gene Fusion Specification <https://fusions.cancervariants.org/en/latest/>`_ when modeling a :ref:`GeneFusion` using this constraint. Specifically by:
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* Representing `Named Gene Components <https://fusions.cancervariants.org/en/latest/nomenclature.html#named-gene-component>`_ as a :ref:`MappableConcept` with the `conceptType` field set to "Gene"; the `Gene Normalizer <https://gene-normalizer.readthedocs.io>`_ can help.
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* Representing `Multiple Possible Gene Components <https://fusions.cancervariants.org/en/latest/nomenclature.html#multiple-possible-gene-component>`_ as a :ref:`UnspecifiedElement` within the Adjacency Constraint. An exhaustive or non-exhaustive list of possible elements can be included as an :ref:`Extension`. We recommend setting the value to be a :ref:`ConceptSet` with the `membershipOperator` field set to "OR".
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* Representing an `Unknown Gene Component <https://fusions.cancervariants.org/en/latest/nomenclature.html#unknown-gene-component>`_ as a :ref:`UnspecifiedElement`.

‎docs/source/concepts/Constraints/CopyChangeConstraint.rst‎

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.. _CopyChangeConstraint:
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Copy Change Constraint
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!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/CopyChangeConstraint.rst
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Examples
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The following are example implementations of Copy Change Constraint:
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.. collapse:: Gain
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_categoricalCnv-ex2
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:language: json
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:lines: 43-46
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.. collapse:: Loss
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_tp53-copy-loss
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:language: json
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:lines: 99-102
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Implementation Guidance
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‎docs/source/concepts/Constraints/CopyCountConstraint.rst‎

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.. _CopyCountConstraint:
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Copy Count Constraint
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!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/CopyCountConstraint.rst
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Examples
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The following are example implementations of CopyCountConstraint:
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.. collapse:: 3 copies
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_categoricalCnv-ex3
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:language: json
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:lines: 21-24
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Implementation Guidance
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‎docs/source/concepts/Constraints/DefiningAlleleConstraint.rst‎

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.. _DefiningAlleleConstraint:
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Defining Allele Constraint
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!!!!!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/DefiningAlleleConstraint.rst
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Examples
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The following are example implementations of DefiningAlleleConstraint:
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.. collapse:: NM_004958.4(MTOR):c.5992_5993del (p.Met1998fs)
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_canonicalAllele-ex1
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:language: json
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:lines: 83-172
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.. collapse:: NC_000001.11:g.1699974C>G
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_canonicalAllele-ex2
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:language: json
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:lines: 37-112
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.. collapse:: EGFR L858R
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_proteinSequenceConsequence-ex1
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:language: json
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:lines: 99-150
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.. collapse:: NM_007294.4(BRCA1):c.5558dup (p.Tyr1853Ter)
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_proteinSequenceConsequence-ex2
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:language: json
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:lines: 69-132
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Implementation Guidance
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‎docs/source/concepts/Constraints/DefiningLocationConstraint.rst‎

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.. _DefiningLocationConstraint:
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Defining Location Constraint
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/DefiningLocationConstraint.rst
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Examples
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The following are example implementations of DefiningLocationConstraint:
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.. collapse:: GRCh38/hg38 7p22.1(chr7:5905831-6014161)x3
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_categoricalCnv-ex1
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:language: json
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:lines: 47-102
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.. collapse:: GRCh38 Xp22.31(chrX:6978350-7594949)x3
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_categoricalCnv-ex3
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:language: json
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:lines: 25-79
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.. collapse:: BRAF V600
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_braf-v600
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:language: json
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Implementation Guidance
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‎docs/source/concepts/Constraints/FeatureContextConstraint.rst‎

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.. _FeatureContextConstraint:
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Feature Context Constraint
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!!!!!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/FeatureContextConstraint.rst
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Examples
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The following are example implementations of FeatureContextConstraint:
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.. collapse:: Gene: TP53
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_tp53-copy-loss
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:language: json
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:lines: 74-98
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.. collapse:: Gene: NRAS
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex1
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:language: json
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:lines: 10-26
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.. collapse:: Gene: BRCA2
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex2
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:language: json
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:lines: 10-26
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.. collapse:: Gene: PIK3CA
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex3
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:language: json
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Implementation Guidance
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‎docs/source/concepts/Constraints/FunctionConstraint.rst‎

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.. _FunctionConstraint:
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Function Constraint
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!!!!!!!!!!!!!!!!!!!!!!
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Definition and Information Model
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.. include:: ../../def/cat-vrs/FunctionConstraint.rst
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Examples
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The following are example implementations of FunctionConstraint:
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.. collapse:: NRAS functionally normal variants
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex1
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:language: json
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:lines: 27-43
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.. collapse:: BRCA2 loss of function variants
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex2
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:language: json
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:lines: 27-43
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.. collapse:: PIK3CA p.R38H
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.. literalinclude:: ../../../../schema/cat-vrs/json/example_functionVariant-ex3
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:language: json
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:lines: 84-100
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Implementation Guidance
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The `functionConsequence` attribute is a :ref:`MappableConcept`, meaning that it should be represented using an externally defined ontology term. We recommend using one of the following defined terms from `The Sequence Ontology <http://www.sequenceontology.org>`_:
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* **dominant negative variant** (`SO:0002052 <http://www.sequenceontology.org/browser/current_release/term/SO:0002052>`_ - dominant_negative_variant): A variant where the mutated gene product adversely affects the other (wild type) gene product.
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* **functionally normal** (`SO:0002219 <http://www.sequenceontology.org/browser/current_release/term/SO:0002219>`_ - functionally_normal): A sequence variant in which the function of a gene product is retained with respect to a reference.
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* **gain of function** (`SO:0002053 <http://www.sequenceontology.org/browser/current_release/term/SO:0002053>`_ - gain_of_function_variant): A sequence variant whereby new or enhanced function is conferred on the gene product.
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* **loss of function** (`SO:0002054 <http://www.sequenceontology.org/browser/current_release/term/SO:0002054>`_ - loss_of_function_variant): A sequence variant whereby the gene product has diminished or abolished function.
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* **loss of heterozygosity** (`SO:0001786 <http://www.sequenceontology.org/browser/current_release/term/SO:0001786>`_ - loss_of_heterozygosity): A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.
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* **polypeptide partial loss of function** (`SO:0001561 <http://www.sequenceontology.org/browser/current_release/term/SO:0001561>`_ - polypeptide_partial_loss_of_function): A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.

‎docs/source/concepts/Constraints/index.rst‎

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.. _constraints:
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Constraints
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!!!!!!!!!!!
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Constraints define rules or sets of rules that a :ref:`Categorical Variant <CategoricalVariant>` must satisfy to qualify as a valid member of the Categorical Variant.
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See :ref:`Constraint` for the abstract base class.
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**Subclasses**
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.. toctree::
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:titlesonly:
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AdjacencyConstraint
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CopyChangeConstraint
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CopyCountConstraint
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DefiningAlleleConstraint
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DefiningLocationConstraint
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FeatureContextConstraint
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FunctionConstraint

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