fix: remove StudyResult from EvidenceLine.hasEvidenceItems and re-r…

…un make all

schema/va-spec/base/def/ClinicalVariantProposition.rst

@@ -76,7 +76,7 @@ Some ClinicalVariantProposition attributes are inherited from :ref:`SubjectVaria
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/EvidenceLine.rst

@@ -88,7 +88,7 @@ Some EvidenceLine attributes are inherited from :ref:`InformationEntity`.
                         .. raw:: html
 
                             <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
-      - :ref:`StudyResult` | :ref:`Statement` | :ref:`EvidenceLine` | :ref:`iriReference`
+      - :ref:`Statement` | :ref:`EvidenceLine` | :ref:`iriReference`
       - 0..m
       - An individual piece of information that was evaluated as evidence in building the argument represented by an Evidence Line.
    *  - directionOfEvidenceProvided

schema/va-spec/base/def/ExperimentalVariantFunctionalImpactProposition.rst

@@ -71,9 +71,9 @@ Some ExperimentalVariantFunctionalImpactProposition attributes are inherited fro
       - 
       - :ref:`iriReference` | :ref:`MappableConcept`
       - 1..1
-      - The sequence feature (typically a gene or gene product) on whose function the impact  of the subject variant is reported.
+      - The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is reported.
    *  - experimentalContextQualifier
       - 
       - :ref:`iriReference` | :ref:`Document` | object
       - 0..1
-      - An assay in which the reported variant functional impact was determined -  providing a specific experimental context in which this effect is asserted to hold.
+      - An assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.

schema/va-spec/base/def/Statement.rst

@@ -82,7 +82,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
       - 
       - :ref:`Proposition`
       - 1..1
-      - A possible fact, the validity of which is assessed and reported by the Statement. A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim. 
+      - A possible fact, the validity of which is assessed and reported by the Statement. A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim.
    *  - direction
       - 
       - string
@@ -100,7 +100,7 @@ Some Statement attributes are inherited from :ref:`InformationEntity`.
                             <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>
       - number
       - 0..1
-      - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. Instructions for how to interpret the menaing of a given score may be gleaned from the method or document referenced in 'specifiedBy' attribute. 
+      - A quantitative score that indicates the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it. Instructions for how to interpret the menaing of a given score may be gleaned from the method or document referenced in 'specifiedBy' attribute.
    *  - classification
       - 
       - :ref:`MappableConcept`

schema/va-spec/base/def/VariantDiagnosticProposition.rst

@@ -61,7 +61,7 @@ Some VariantDiagnosticProposition attributes are inherited from :ref:`ClinicalVa
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantOncogenicityProposition.rst

@@ -61,7 +61,7 @@ Some VariantOncogenicityProposition attributes are inherited from :ref:`Clinical
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantPathogenicityProposition.rst

@@ -61,7 +61,7 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Clinica
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
@@ -86,7 +86,7 @@ Some VariantPathogenicityProposition attributes are inherited from :ref:`Clinica
       - 
       - :ref:`MappableConcept`
       - 0..1
-      - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition. 
+      - Reports the penetrance of the pathogenic effect - i.e. the extent to which the variant impact is expressed by individuals carrying it as a measure of the proportion of carriers exhibiting the condition.
    *  - modeOfInheritanceQualifier
       - 
       - :ref:`MappableConcept`

schema/va-spec/base/def/VariantPrognosticProposition.rst

@@ -61,7 +61,7 @@ Some VariantPrognosticProposition attributes are inherited from :ref:`ClinicalVa
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`

schema/va-spec/base/def/VariantTherapeuticResponseProposition.rst

@@ -61,7 +61,7 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`C
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
       - 0..1
-      - Reports a gene impacted by the variant, which may contribute to the association  described in the Proposition.
+      - Reports a gene impacted by the variant, which may contribute to the association described in the Proposition.
    *  - alleleOriginQualifier
       - 
       - :ref:`MappableConcept` | :ref:`iriReference`
@@ -86,4 +86,4 @@ Some VariantTherapeuticResponseProposition attributes are inherited from :ref:`C
       - 
       - :ref:`Condition` | :ref:`iriReference`
       - 1..1
-      - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response propositions. 
+      - Reports the disease context in which the variant's association with therapeutic sensitivity or resistance is evaluated. Note that this is a required qualifier in therapeutic response propositions.

schema/va-spec/base/json/CohortAlleleFrequencyStudyResult

@@ -46,7 +46,7 @@
             }
          ],
          "description": "A specification that describes all or part of the process that led to creation of the Information Entity",
-         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a  method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "contributions": {
          "type": "array",

schema/va-spec/base/json/EvidenceLine

@@ -47,7 +47,7 @@
             }
          ],
          "description": "A specification that describes all or part of the process that led to creation of the Information Entity",
-         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a  method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "contributions": {
          "type": "array",
@@ -108,9 +108,6 @@
          "ordered": false,
          "items": {
             "anyOf": [
-               {
-                  "$ref": "/ga4gh/schema/va-spec/1.x/base/json/StudyResult"
-               },
                {
                   "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
                },

schema/va-spec/base/json/ExperimentalVariantFunctionalImpactProposition

@@ -49,7 +49,7 @@
             }
          ],
          "description": "A variant that is the subject of the Proposition.",
-         "$comment": "In profiles for most VA-Spec implementations, the subject will be a some type of genetic  variation. However, the Core VA model is domain-agnostic, and supports Propositions about any type of Entity. Some data providers may want to make statements about other entities or concepts that represent evidence for a Propositions about genetic variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
+         "$comment": "In profiles for most VA-Spec implementations, the subject will be a some type of genetic variation. However, the Core VA model is domain-agnostic, and supports Propositions about any type of Entity. Some data providers may want to make statements about other entities or concepts that represent evidence for a Propositions about genetic variation (e.g. a statement that a gene is valid for some disease is one type of evidence that may support the pathogenicity of a variant that affects that gene)."
       },
       "type": {
          "type": "string",
@@ -73,11 +73,11 @@
                "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
-         "description": "The sequence feature (typically a gene or gene product) on whose function the impact  of the subject variant is reported.",
+         "description": "The sequence feature (typically a gene or gene product) on whose function the impact of the subject variant is reported.",
          "$comment": "The object of a Proposition can be any Entity or concept that is related to the subject. When the subject is a genetic variation, the object is often a disease, phenotype, therapeutic intervention, or gene."
       },
       "experimentalContextQualifier": {
-         "description": "An assay in which the reported variant functional impact was determined -  providing a specific experimental context in which this effect is asserted to hold.",
+         "description": "An assay in which the reported variant functional impact was determined - providing a specific experimental context in which this effect is asserted to hold.",
          "anyOf": [
             {
                "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
@@ -88,7 +88,7 @@
             {
                "type": "object",
                "additionalProperties": true,
-               "$comment": "It is expected that non-Document objects will conform to externally-maintained  community schemas for representing experimental context data."
+               "$comment": "It is expected that non-Document objects will conform to externally-maintained community schemas for representing experimental context data."
             }
          ]
       }

schema/va-spec/base/json/ExperimentalVariantFunctionalImpactStudyResult

@@ -93,7 +93,7 @@
             }
          ],
          "description": "The assay that was performed to generate the reported functional impact score.",
-         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a  method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
+         "$comment": "Examples: a specific experimental protocol or data analysis specification that describes how data were generated; an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification; a method for using electron microscopy to image cell membrane proteins. Note that this attribute captures a specific *instance* of a specification or method (e.g. the specific electron microscopy method described in https://doi.org/10.1002/cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. 'Transmission Electron Microscopy')."
       },
       "sourceDataSet": {
          "$ref": "/ga4gh/schema/va-spec/1.x/base/json/DataSet",