From e88e94a6a287b07abfd26ef29b1f364ef600b98a Mon Sep 17 00:00:00 2001
From: Michael Baudis <675030+mbaudis@users.noreply.github.com>
Date: Mon, 18 Mar 2024 14:09:29 +0100
Subject: [PATCH] css, another example...

---
 docs/css/theme_overrides.css | 59 ++++++++++++++++++++++++++++++++++++
 docs/index.md                |  6 ++--
 docs/use-case-examples.md    | 19 ++++++++++++
 mkdocs.yml                   |  4 ++-
 4 files changed, 85 insertions(+), 3 deletions(-)
 create mode 100644 docs/css/theme_overrides.css

diff --git a/docs/css/theme_overrides.css b/docs/css/theme_overrides.css
new file mode 100644
index 0000000..a31b897
--- /dev/null
+++ b/docs/css/theme_overrides.css
@@ -0,0 +1,59 @@
+:root {
+  --md-accent-fg-color: #076d63;
+}
+
+.md-grid {
+  max-width: 1200px; 
+}
+
+.md-header__source {
+    background-image: url("/img/elixir-white-48x36.png");
+    background-repeat: no-repeat;
+    background-position: right;   
+}
+
+div.figcaption {
+    text-align: justify;
+    line-height:  1.2em;
+    font-size: 0.8em;
+    margin: 0 30px 18px 30px;
+}
+
+.md-typeset h1 {
+    line-height:  1.2em;
+    margin: 0 0 24px 0;
+}
+
+.md-typeset ul li {
+    line-height:  1.4em;
+    margin-bottom: 0.2em;
+}
+
+
+h2 {
+    color: var(--md-accent-fg-color);
+    border-top:  var(--md-accent-fg-color) thin solid;
+    border-bottom:  var(--md-accent-fg-color) thin solid;
+}
+
+div.tabbed-set {
+    background-color:  #fafafa;
+}
+
+.tabbed-content {
+    padding:  5px;
+}
+
+li li {
+    list-style-type: circle;
+}
+
+li li li {
+    list-style-type: "–";
+    font-size: 0.9em;
+}
+
+.mermaid {
+  display: flex;
+  justify-content: center;
+}
diff --git a/docs/index.md b/docs/index.md
index 7bf6204..1e8342c 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -15,8 +15,10 @@ The outcome of this scout would be a document summarising points 1-3, and buildi
 
 ## Material & References
 
-* Beacon v2 [Variant Queries documenattion](http://docs.genomebeacons.org/variant-queries/#genomic-variant-queries)
+* Beacon v2 [Variant Queries documentation](http://docs.genomebeacons.org/variant-queries/#genomic-variant-queries)
 * Previous [Beacon Scouts: Genomic Variants Use Cases & Examples](https://docs.google.com/document/d/1cwwRQ2PtlN1dBffCugdkbSHWCPmLgLkADd-5mu-rVAw/edit)
+* [VRS data model](https://vrs.ga4gh.org/en/latest/terms_and_model.html)
+
 * ELIXIR hCNV [CNV type comparison matrix](https://cnvar.org/resources/CNV-annotation-standards/)
 * Experimental Factor Ontology [CNVs](https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0030066?lang=en)
-* Sequence Ontology [sequence_variant]](http://sequenceontology.org/browser/current_release/term/SO:0001060)
\ No newline at end of file
+* Sequence Ontology [sequence_variant](http://sequenceontology.org/browser/current_release/term/SO:0001060)
\ No newline at end of file
diff --git a/docs/use-case-examples.md b/docs/use-case-examples.md
index ba6a0f6..8fd0e66 100644
--- a/docs/use-case-examples.md
+++ b/docs/use-case-examples.md
@@ -29,4 +29,23 @@ For the interpretation of the "deletion" parameter see above.
 
 --------------------------------------------------------------------------------
 
+## Copy number gains involving the whole locus (chr2:54,700,000-63,900,000)
+
+The query has to indicate the involved genomic region by positions as well as the
+type of change. Here, matched duplication events start 5\` of the region and end 3\`
+of it.
+
+Besides the positions, this requires knowledge about the maximum value of the
+reference base (or use of  a very large one exceeding chromosome size; this example
+here uses an "2nd end position equal to chr2 + 1" value).
+
+While the example uses `SO:0001742` for `copy_number_gain` the EFO term use
+(`EFO:0030070`: `copy number gain`) should be preferred since the EFO terms provide
+a more granular expressivity and are referenced in the [VRS definitions](https://vrs.ga4gh.org/en/latest/terms_and_model.html#systemic-variation).
+
+```
+?referenceName=refseq:NC_000002.12&start=0,54700000&end=63900000,242193529&variantType=SO:0001742
+```
+
+--------------------------------------------------------------------------------
 ==TBD==
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 6ca6548..691be7d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -17,7 +17,9 @@ nav:
   - Use Cases: use-case-examples
   - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas
 
-###############################################################################
+#<--------------------------- / Navigation ----------------------------------->#
+
+extra_css: [css/theme_overrides.css]
 
 markdown_extensions:
     - toc: