story board

9 files changed, 34 insertions, 3 deletions

diff --git a/story-boards/starting-from-known-gene/generate.sh b/story-boards/starting-from-known-gene/generate.sh
index c5d4d3d..c44558e 100755
--- a/story-boards/starting-from-known-gene/generate.sh
+++ b/story-boards/starting-from-known-gene/generate.sh
@@ -1,10 +1,18 @@
 #!/bin/bash
 
-ruby ../../scripts/screenshot.rb --url "http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2"  --out genewiki.png --extract 1200x500+0+0
+ruby ../../scripts/screenshot.rb --out trait-1419076_a_at.png --url "https://genenetwork.org/show_trait?trait_id=1419076_a_at&dataset=HC_M2_0606_P"
 
 exit 1
+
+ruby ../../scripts/screenshot.rb --out search-brca2.png --extract 1200x330+0+330 --url "https://genenetwork.org/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=BRCA2&search_terms_and=&FormID=searchResult"
+
+ruby ../../scripts/screenshot.rb --url "http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2"  --out genewiki.png --extract 1200x500+0+0
+
 ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/" --out genenetwork-home.png
 convert -extract 800x100+0+0 genenetwork-home.png global-search.png
+convert -extract 570x350+0+90 genenetwork-home.png search1.png
+convert -extract 570x500+0+90 genenetwork-home.png search.png
+
 
 ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/gsearch?type=gene&terms=Brca2" --out global-search-gene.png --extract 800x300+0+0
 
diff --git a/story-boards/starting-from-known-gene/genewiki.png b/story-boards/starting-from-known-gene/genewiki.png
index 22d7580..eb90846 100644
--- a/story-boards/starting-from-known-gene/genewiki.png
+++ b/story-boards/starting-from-known-gene/genewiki.png
diff --git a/story-boards/starting-from-known-gene/global-search.png b/story-boards/starting-from-known-gene/global-search.png
index b2cf1ef..90841ad 100644
--- a/story-boards/starting-from-known-gene/global-search.png
+++ b/story-boards/starting-from-known-gene/global-search.png
diff --git a/story-boards/starting-from-known-gene/search-brca2.png b/story-boards/starting-from-known-gene/search-brca2.png
new file mode 100644
index 0000000..e08f67d
--- /dev/null
+++ b/story-boards/starting-from-known-gene/search-brca2.png
diff --git a/story-boards/starting-from-known-gene/search.png b/story-boards/starting-from-known-gene/search.png
new file mode 100644
index 0000000..ce286e7
--- /dev/null
+++ b/story-boards/starting-from-known-gene/search.png
diff --git a/story-boards/starting-from-known-gene/search1.png b/story-boards/starting-from-known-gene/search1.png
new file mode 100644
index 0000000..f324d52
--- /dev/null
+++ b/story-boards/starting-from-known-gene/search1.png
diff --git a/story-boards/starting-from-known-gene/search2.png b/story-boards/starting-from-known-gene/search2.png
new file mode 100644
index 0000000..8e05ef4
--- /dev/null
+++ b/story-boards/starting-from-known-gene/search2.png
diff --git a/story-boards/starting-from-known-gene/starting-from-known-gene.md b/story-boards/starting-from-known-gene/starting-from-known-gene.md
index 2abd7a1..523d4b0 100644
--- a/story-boards/starting-from-known-gene/starting-from-known-gene.md
+++ b/story-boards/starting-from-known-gene/starting-from-known-gene.md
@@ -26,11 +26,34 @@ GeneNetwork ignores case by default. In a search use quotes to search case sensi
 
 # Find the GeneNetwork genewiki entry
 
-GeneNetwork maintains info on gene entries. For example for BRCA2:
+GeneNetwork maintains info on gene entries. For example on the above trait page for 1448542_at/BRCA2 the [genewiki] button takes you to:
 
 [![Genewiki](./genewiki.png "Genewiki for Brca2")](http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2)
 
-FIXME: we aim to move this functionality to markdown
+FIXME: @zsloan we aim to move this functionality to GN2/markdown
+
+# Looking experiments that
+
+On the GN home page we find advanced search routines
+
+[![GN Search1](./search1.png "Genenetwork search1")](https://genenetwork.org/)
+
+In the 'Get any' box type `BRCA2' and hit [Search] to find all traits that mention Brca2 for the matching datasets (here Hippocampus mRNA) resulting in
+
+[![BRCA2](./search-brca2.png "BRCA2")](http://genenetwork.org/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=BRCA2&search_terms_and=&FormID=searchResult)
+
+So, for this dataset 7 results are shown with interesting QTL scores.
+
+Click on the trait `1419076_a_at` that is annotated as `Brca2` on Chr5: 150.569266  with a QTL on Chr1: 191.908117 and we get to the powerful mapping page
+
+[![1419076_a_at](./trait-1419076_a_at.png "1419076_a_at")](https://genenetwork.org/show_trait?trait_id=1419076_a_at&dataset=HC_M2_0606_P)
+
+As we picked this trait from an RNA dataset 1419076_a_at likely is a gene expression trait. Clicking on link [Hippocampus Consortium M430v2 (Jun06)] tells us is is a dataset on 'Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource.'
+
+FIXME: @pjotrp: add a link out on the mapping page to wikidata
+FIXME: @pjotrp: [UCSC] link is pointing to CHR12
+FIXME: @pjotrp: we need a link to uniprot(!)
+
 
 # TODO
 
diff --git a/story-boards/starting-from-known-gene/trait-1419076_a_at.png b/story-boards/starting-from-known-gene/trait-1419076_a_at.png
new file mode 100644
index 0000000..ecd3013
--- /dev/null
+++ b/story-boards/starting-from-known-gene/trait-1419076_a_at.png