From d5b148199fda41ff1b1a1e85a5cea808769c3e15 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Wed, 4 Dec 2024 16:52:47 -0500 Subject: [PATCH] updated domain-entities to complete links needed for remaining TU links. --- .../base-profiles/proposition-profiles.rst | 7 ++++ .../core-information-model/data-types.rst | 32 ++++++++++--------- .../domain-entities/conditions/disease.rst | 8 ++++- .../domain-entities/conditions/index.rst | 7 +++- .../domain-entities/conditions/phenotype.rst | 8 ++++- .../entities/domain-entities/gene.rst | 8 ++++- .../entities/domain-entities/index.rst | 3 +- .../combination-therapy.rst | 5 --- .../therapeutic-procedures/index.rst | 17 ---------- .../therapeutic-action.rst | 4 --- .../therapeutic-agent.rst | 4 --- .../therapeutic-substitute-group.rst | 4 --- .../domain-entities/therapeutics/drug.rst | 12 +++++++ .../domain-entities/therapeutics/index.rst | 21 ++++++++++++ .../therapeutics/procedure.rst | 12 +++++++ .../therapeutics/therapy-group.rst | 6 ++++ 16 files changed, 103 insertions(+), 55 deletions(-) delete mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst delete mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/index.rst delete mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst delete mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst delete mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst create mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst create mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst create mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutics/procedure.rst create mode 100644 docs/source/core-information-model/entities/domain-entities/therapeutics/therapy-group.rst diff --git a/docs/source/base-profiles/proposition-profiles.rst b/docs/source/base-profiles/proposition-profiles.rst index 46111d16..dde7f872 100644 --- a/docs/source/base-profiles/proposition-profiles.rst +++ b/docs/source/base-profiles/proposition-profiles.rst @@ -122,3 +122,10 @@ Variant Prognostic Proposition .. include:: ../def/va-spec/VariantPrognosticProposition.rst +.. _experimental-variant-functional-impact-proposition: + +Experimental Variant Functional Impact Proposition +################################################## + +.. include:: ../def/va-spec/ExperimentalVariantFunctionalImpactProposition.rst + \ No newline at end of file diff --git a/docs/source/core-information-model/data-types.rst b/docs/source/core-information-model/data-types.rst index a5721b80..9f967289 100644 --- a/docs/source/core-information-model/data-types.rst +++ b/docs/source/core-information-model/data-types.rst @@ -3,15 +3,8 @@ Data Types !!!!!!!!!! -Complex Data Types -################### - -.. _Coding: - -Coding -****** - -.. include:: ../def/gks-core/Coding.rst +General Purpose Data Types +########################## .. _Extension: @@ -19,21 +12,30 @@ Extension ********* .. include:: ../def/gks-core/Extension.rst +.. _MappableConcept: -.. _RecordMetadata: +MappableConcept +*************** -RecordMetadata -************** +.. include:: ../def/gks-core/MappableConcept.rst -.. include:: ../def/va-spec/RecordMetadata.rst +.. _ConceptMapping: ConceptMapping ************** .. include:: ../def/gks-core/ConceptMapping.rst -Simple Data Types -################### +.. _Coding: + +Coding +****** + +.. include:: ../def/gks-core/Coding.rst + + +Primitive Data Types +#################### .. _code: diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst b/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst index b22d68a2..0049552b 100644 --- a/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst +++ b/docs/source/core-information-model/entities/domain-entities/conditions/disease.rst @@ -3,4 +3,10 @@ Disease !!!!!!! -.. include:: ../../../../../../schema/domain-entities/def/Disease.rst +We defer to the adopters to use the disease naming authority of their choice +(e.g. OMIM, MONDO, etc.) to share a representation of a Disease concept using +the :ref:`MappableConcept` data type. + +NOTE: **conceptType** should be set to "Disease". + +.. include:: ../../../../def/gks-core/MappableConcept.rst diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/index.rst b/docs/source/core-information-model/entities/domain-entities/conditions/index.rst index 4e24fdb3..6e1b0ce4 100644 --- a/docs/source/core-information-model/entities/domain-entities/conditions/index.rst +++ b/docs/source/core-information-model/entities/domain-entities/conditions/index.rst @@ -6,7 +6,12 @@ Condition .. include:: ../../../../def/va-spec/Condition.rst -**Subclasses** +Condition Types +############### + +**Disease** and **Phenotype** are :ref:`MappableConcept` example +condition types (aka traits) for the atomic representation of a trait. +MappableConcept may be used for other condition types if appropriate. .. toctree:: :titlesonly: diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/phenotype.rst b/docs/source/core-information-model/entities/domain-entities/conditions/phenotype.rst index e5375c57..fc8e7b14 100644 --- a/docs/source/core-information-model/entities/domain-entities/conditions/phenotype.rst +++ b/docs/source/core-information-model/entities/domain-entities/conditions/phenotype.rst @@ -3,4 +3,10 @@ Phenotype !!!!!!!!! -.. include:: ../../../../../../schema/domain-entities/def/Phenotype.rst +We defer to the adopters to use the phenotype naming authority of their choice +(e.g. HPO, etc.) to share a representation of a Phenotype concept using +the :ref:`MappableConcept` data object. + +NOTE: **conceptType** should be set to "Phenotype". + +.. include:: ../../../../def/gks-core/MappableConcept.rst diff --git a/docs/source/core-information-model/entities/domain-entities/gene.rst b/docs/source/core-information-model/entities/domain-entities/gene.rst index 99f013f2..4ea86c71 100644 --- a/docs/source/core-information-model/entities/domain-entities/gene.rst +++ b/docs/source/core-information-model/entities/domain-entities/gene.rst @@ -3,4 +3,10 @@ Gene !!!! -.. include:: ../../../def/va-spec/Gene.rst +We defer to the adopters to use the gene naming authority of their choice +(e.g. HGNC, ENTREZ-GENE, etc.) to share a representation of a Gene entity using +the MappableConcept data object. + +NOTE: **conceptType** should be set to "Gene". + +.. include:: ../../../../def/gks-core/MappableConcept.rst diff --git a/docs/source/core-information-model/entities/domain-entities/index.rst b/docs/source/core-information-model/entities/domain-entities/index.rst index 0b62f8af..d9e11d4a 100644 --- a/docs/source/core-information-model/entities/domain-entities/index.rst +++ b/docs/source/core-information-model/entities/domain-entities/index.rst @@ -19,7 +19,6 @@ Note that these are minimally specified models at present, which will be evolved .. toctree:: :titlesonly: - gene conditions/index - therapeutic-procedures/index + therapeutics/index diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst b/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst deleted file mode 100644 index 6868a24e..00000000 --- a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/combination-therapy.rst +++ /dev/null @@ -1,5 +0,0 @@ -Combination Therapy -!!!!!!!!!!!!!!!!!!! - - -.. include:: ../../../../../../schema/domain-entities/def/CombinationTherapy.rst diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/index.rst b/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/index.rst deleted file mode 100644 index 0ce1d9f3..00000000 --- a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -.. _TherapeuticProcedure: - -Therapeutic Procedure -!!!!!!!!!!!!!!!!!!!!! - -.. include:: ../../../../../../schema/domain-entities/def/TherapeuticProcedure.rst - - -**Subclasses** - -.. toctree:: - :titlesonly: - - therapeutic-agent - therapeutic-action - combination-therapy - therapeutic-substitute-group diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst b/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst deleted file mode 100644 index e1bc2e91..00000000 --- a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-action.rst +++ /dev/null @@ -1,4 +0,0 @@ -Therapeutic Action -!!!!!!!!!!!!!!!!!! - -.. include:: ../../../../../../schema/domain-entities/def/TherapeuticAction.rst diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst b/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst deleted file mode 100644 index 33c60c30..00000000 --- a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-agent.rst +++ /dev/null @@ -1,4 +0,0 @@ -Therapeutic Agent -!!!!!!!!!!!!!!!!! - -.. include:: ../../../../../../schema/domain-entities/def/TherapeuticAgent.rst diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst b/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst deleted file mode 100644 index 30d09887..00000000 --- a/docs/source/core-information-model/entities/domain-entities/therapeutic-procedures/therapeutic-substitute-group.rst +++ /dev/null @@ -1,4 +0,0 @@ -Therapeutic Substitute Group -!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -.. include:: ../../../../../../schema/domain-entities/def/TherapeuticSubstituteGroup.rst diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst new file mode 100644 index 00000000..2b3e7950 --- /dev/null +++ b/docs/source/core-information-model/entities/domain-entities/therapeutics/drug.rst @@ -0,0 +1,12 @@ +.. _Drug: + +Drug +!!!! + +We defer to the adopters to use the drug naming authority of their choice +(e.g. NCIT, RXNORM, etc.) to share a representation of a Drug concept using +the :ref:`MappableConcept` data object. + +NOTE: **conceptType** should be set to "Drug". + +.. include:: ../../../../def/gks-core/MappableConcept.rst \ No newline at end of file diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst new file mode 100644 index 00000000..e7217b6f --- /dev/null +++ b/docs/source/core-information-model/entities/domain-entities/therapeutics/index.rst @@ -0,0 +1,21 @@ +.. _Therapeutic: + +Therapeutic +!!!!!!!!!!! + +.. include:: ./../../../def/va-spec/Therapeutic.rst + +Therapeutic Types +################# + +**Drug** and **Procedure** are :ref:`MappableConcept` example +therapeutic types for the atomic representation of a therapy. +MappableConcept may be used for other therapy types if appropriate +(i.e. behavioral-intervention, etc..). + +.. toctree:: + :titlesonly: + + drug + procedure + therapy-group diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/procedure.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/procedure.rst new file mode 100644 index 00000000..92e3a21c --- /dev/null +++ b/docs/source/core-information-model/entities/domain-entities/therapeutics/procedure.rst @@ -0,0 +1,12 @@ +.. _Procedure: + +Procedure +!!!!!!!!! + +We defer to the adopters to use the procedure naming authority of their choice +(e.g. NCIT, etc.) to share a representation of a Procedure concept using +the :ref:`MappableConcept` data object. + +NOTE: **conceptType** should be set to "Procedure". + +.. include:: ../../../../def/gks-core/MappableConcept.rst \ No newline at end of file diff --git a/docs/source/core-information-model/entities/domain-entities/therapeutics/therapy-group.rst b/docs/source/core-information-model/entities/domain-entities/therapeutics/therapy-group.rst new file mode 100644 index 00000000..1bf6b57f --- /dev/null +++ b/docs/source/core-information-model/entities/domain-entities/therapeutics/therapy-group.rst @@ -0,0 +1,6 @@ +.. _TherapyGroup: + +Therapy Group +!!!!!!!!!!!!! + +.. include:: ../../../../def/va-spec/TherapyGroup.rst \ No newline at end of file