replaced old icon fontawesome aliases w/ generated cvc aliases

Author: jmcmichael

docs/_static/css/theme_overrides.css

@@ -18,7 +18,7 @@ table.docutils th {
 }
 
 table.docutils th p {
-  line-height: 1em !important;
+  line-height: 1.2em !important;
   font-weight: normal !important;
   font-size: 1em !important;
   font-style: oblique;
@@ -28,3 +28,6 @@ table.docutils th p {
 table.docutils td {
   padding: 6px 8px !important;
 }
+table.docutils td p {
+  line-height: 1.2em !important;
+}

docs/model/evidence/direction.rst

@@ -1,3 +1,5 @@
+.. include:: /generated/civic.docs-aliases.rst
+
 .. _evidence-direction:
 
 Direction
@@ -14,92 +16,100 @@ Evidence Direction interpretation differs slightly depending on the Evidence Typ
 
 .. rubric:: Direction for Predictive Evidence
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study supports this variant’s response to a drug
+     - |attribute-supports|
+     - Experiment or study supports the variant's response to a drug
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study does not support, or was inconclusive of an interaction between the variant and a drug
+     - |attribute-doesnotsupport|
+     - Experiment or study does not support, or was inconclusive of an interaction between the variant and a drug
 
 
 .. rubric:: Direction for Diagnostic Evidence
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study supports variant’s impact on the diagnosis of disease or subtype
+     - |attribute-supports|
+     - Experiment or study supports the variant's impact on the diagnosis of disease or subtype
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study does not support the variant’s impact on diagnosis of disease or subtype
+     - |attribute-doesnotsupport|
+     - Experiment or study does not support the variant's impact on diagnosis of disease or subtype
 
 .. rubric:: Direction for Prognostic Evidence
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study supports a variant’s impact on prognostic outcome
+     - |attribute-supports|
+     - Experiment or study supports the variant's impact on prognostic outcome
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study does not support a prognostic association between variant and outcome
+     - |attribute-doesnotsupport|
+     - Experiment or study does not support a prognostic association between variant and outcome
 
 .. rubric:: Direction for Predisposing Evidence (where Significance is Predisposition)
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study may contribute to a pathogenic classification (final determination at the Assertion level)
+     - |attribute-supports|
+     - Suggests a pathogenic or a protective role for a germline variant in cancer
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study may contribute to a benign classification (final determination at the Assertion level)
+     - |attribute-doesnotsupport|
+     - Supports a benign (for Predisposition) or lack of protective (for Protectiveness) role for a germline variant in cancer.
 
-.. rubric:: Direction for Oncogenic Evidence (where Significance is Oncogenicity)
+.. rubric:: Direction for Functional Evidence
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study may contribute to an oncogenic classification (final determination at the Assertion level)
+     - |attribute-supports|
+     - Experiment or study supports the variant causing alteration or non-alteration of the gene product function
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study may contribute to a benign classification (final determination at the Assertion level)
+     - |attribute-doesnotsupport|
+     - Experiment or study does not support the variant causing alteration or non-alteration of the gene product function
 
-.. rubric:: Direction for Functional Evidence
+.. rubric:: Direction for Oncogenic Evidence (where Significance is Oncogenicity)
 .. list-table::
-   :widths: 10 5 85
+   :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Direction
      - Symbol
      - Definition
    * - Supports
-     - |thumbs-up|
-     - The experiment or study supports this variant causing alteration or non-alteration of the gene product function
+     - |attribute-supports|
+     - Supports an oncogenic or protective role for a somatic variant.
    * - Does not support
-     - |thumbs-down|
-     - The experiment or study does not support this variant causing alteration or non-alteration of the gene product function
-
+     - |attribute-doesnotsupport|
+     - Supports a benign (for Oncogenicity) or lack of protective (for Protectiveness) role for a somatic variant in cancer.
+   * - Not Applicable
+     - |attribute-na|
+     - Not applicable for Oncogenic Evidence Type

docs/model/evidence/origin.rst

@@ -1,3 +1,5 @@
+.. include:: /generated/civic.docs-aliases.rst
+
 .. _evidence-origin:
 
 Origin
@@ -23,27 +25,28 @@ Population frequencies should be based on current population databases (e.g., gn
 .. list-table::
    :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Origin
      - Symbol
      - Description
    * - Somatic
-     - |ellipsis-h|
+     - |attribute-somatic|
      - Highest priority variants in CIViC. May include presumed somatic variants largely driven by the usage in the original publication but should be approached with caution in instances of tumor-only analysis. Includes fusions.
    * - Rare Germline
-     - |ellipsis-v|
+     - |attribute-raregermline|
      - Consist of heritable rare variants. Generally, <1% of the population relevant to the publication being cited.
    * - Common Germline
-     - |signal|
+     - |attribute-commongermline|
      - Defined as variants with >1% allele frequency in the population relevant to the publication where the evidence is derived. Are welcome in CIViC, however, generally considered low priority for curation efforts.
    * - Combined
-     - ||
+     - |attribute-combined|
      - Variants in the corresponding Complex Molecular Profile have heterogeneous/multiple origins.
    * - Unknown
-     - |question-circle|
+     - |attribute-unknown|
      - May be used in instances where the publication is ambiguous about the origin of the variant although ordinarily an origin would be known (e.g., tumor-only analysis, analyses including both germline and somatic variants).
    * - N/A
-     - |times-circle-o|
+     - |attribute-na|
      - For variants such as 'Expression' where a germline or somatic origin is not applicable.
 
 .. rubric:: Examples

docs/model/evidence/significance.rst

@@ -1,6 +1,6 @@
-.. _evidence-significance:
+.. include:: /generated/civic.docs-aliases.rst
 
-.. include:: /cvc-icon-aliases.rst
+.. _evidence-significance:
 
 Significance
 ============
@@ -13,116 +13,119 @@ The available options for Significance depend on the Evidence Type selected for
 .. rubric:: Significance for Predictive Evidence
 .. list-table::
    :widths: 25 5 70
-   :header-rows: 0
+   :header-rows: 1
+   :class: cvc-icon-table
 
    * - Significance
      - Symbol
      - Definition
    * - Sensitivity/Response
-     - |benign|
+     - |attribute-sensitivityresponse|
      - Associated with a clinical or preclinical response to treatment
    * - Reduced Sensitivity
-     - |betteroutcome|
+     - |attribute-reducedsensitivity|
      - Response to treatment is lower than seen in other treatment contexts
    * - Resistance
-     - |ban|
+     - |attribute-resistance|
      - Associated with clinical or preclinical resistance to treatment
    * - Adverse Response
-     - |fire|
+     - |attribute-adverseresponse|
      - Associated with an adverse response to drug treatment
    * - N/A
-     - |times-circle-o|
+     - |attribute-na|
      - Variant does not inform clinical interpretation
 
 .. rubric:: Significance for Diagnostic Evidence
 .. list-table::
    :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Significance
      - Symbol
      - Definition
    * - Positive
-     - |plus-circle|
+     - |attribute-positive|
      - Associated with diagnosis of disease or subtype
    * - Negative
-     - |minus-circle|
+     - |attribute-negative|
      - Associated with lack of disease or subtype
 
 .. rubric:: Significance for Prognostic Evidence
 .. list-table::
    :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Significance
      - Symbol
      - Definition
    * - Better Outcome
-     - |arrow-circle-up|
+     - |attribute-betteroutcome|
      - Demonstrates better than expected clinical outcome
    * - Poor Outcome
-     - |arrow-circle-down|
+     - |attribute-pooroutcome|
      - Demonstrates worse than expected clinical outcome
    * - N/A
-     - |times-circle-o|
+     - |attribute-na|
      - Variant does not inform clinical action
 
 .. rubric:: Significance for Predisposing Evidence
 .. list-table::
    :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Significance
      - Symbol
      - Definition
    * - Predisposition
-     - |times-circle-o|
-     - Evidence may contribute to an interpretation of pathogenic/benign at the assertion level
-   * - Protectiveness
-     - |times-circle-o|
-     - Presence of a germline molecular profile reduces the chance of cancer
-
-.. rubric:: Significance for Oncogenic Evidence
-.. list-table::
-   :widths: 25 5 70
-   :header-rows: 1
-
-   * - Significance
-     - Symbol
-     - Definition
-   * - Oncogenicity
-     - |times-circle-o|
-     - Evidence may contributes to an interpretation of oncogenic/benign at the assertion level
+     - |attribute-predisposition|
+     - Germline variant has predisposing potential for cancer, and may meet select ACMG/AMP criteria supporting pathogenic or benign classification.
    * - Protectiveness
-     - |times-circle-o|
-     - Presence of a somatic molecular profile reduces the chance of cancer
-
+     - |attribute-protectiveness|
+     - Germline variant has properties that protect individuals from acquiring cancer.
 
 .. rubric:: Significance for Functional Evidence
 .. list-table::
    :widths: 25 5 70
    :header-rows: 1
+   :class: cvc-icon-table
 
    * - Significance
      - Symbol
      - Definition
    * - Gain of Function
-     - |arrow-circle-up|
-     - A sequence variant whereby enhanced function is conferred on the gene product
+     - |attribute-gainoffunction|
+     - Sequence variant confers an increase in normal gene function
    * - Loss of Function
-     - |arrow-circle-down|
-     - A sequence variant whereby the gene product has diminished or abolished function
+     - |attribute-lossoffunction|
+     - Sequence variant confers a diminished or abolished function
    * - Unaltered Function
-     - |arrows-h|
-     - A sequence variant whereby the function of the gene product is unchanged
+     - |attribute-unalteredfunction|
+     - Gene product of sequence variant is unchanged
    * - Neomorphic
-     - |exclamation-circle|
+     - |attribute-neomorphic|
      - Sequence variant creates a novel function
    * - Dominant Negative
-     - |expand|
-     - Sequence variant abolishes wild type allele function
+     - |attribute-dominantnegative|
+     - Sequence variant abrogates function of wildtype allele gene product
    * - Unknown
-     - |sign-out|
-     - A functional variant that cannot be precisely defined by gain-of-function, loss-of-function, or unaltered function
+     - |attribute-unknown|
+     - Sequence variant that cannot be precisely defined by the other listed categories
 
+.. rubric:: Significance for Oncogenic Evidence
+.. list-table::
+   :widths: 25 5 70
+   :header-rows: 1
+   :class: cvc-icon-table
 
+   * - Significance
+     - Symbol
+     - Definition
+   * - Oncogenicity
+     - |attribute-oncogenicity|
+     - Somatic variant has oncogenic potential for driving cancer, and may meet select ClinGen/CGC/VICC criteria supporting pathogenic or benign classification.
+   * - Protectiveness
+     - |attribute-protectiveness|
+     - Somatic variant has a protective role against cancer.