From 11d55a97792c91ce4b961363db9d852ee6031262 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 17 Nov 2021 06:29:25 -0600 Subject: generate screen shots --- .../starting-from-known-gene/gene-aliases.png | Bin 41086 -> 97534 bytes .../starting-from-known-gene/genenetwork-home.png | Bin 0 -> 168318 bytes .../starting-from-known-gene/genenetwork.png | Bin 168318 -> 0 bytes story-boards/starting-from-known-gene/generate.sh | 7 +++++- .../global-search-gene.png | Bin 47303 -> 55147 bytes .../starting-from-known-gene/global-search.png | Bin 0 -> 12151 bytes .../starting-from-known-gene.md | 27 ++++++--------------- 7 files changed, 14 insertions(+), 20 deletions(-) create mode 100644 story-boards/starting-from-known-gene/genenetwork-home.png delete mode 100644 story-boards/starting-from-known-gene/genenetwork.png create mode 100644 story-boards/starting-from-known-gene/global-search.png diff --git a/story-boards/starting-from-known-gene/gene-aliases.png b/story-boards/starting-from-known-gene/gene-aliases.png index 902723c..a5c544d 100644 Binary files a/story-boards/starting-from-known-gene/gene-aliases.png and b/story-boards/starting-from-known-gene/gene-aliases.png differ diff --git a/story-boards/starting-from-known-gene/genenetwork-home.png b/story-boards/starting-from-known-gene/genenetwork-home.png new file mode 100644 index 0000000..06c16f3 Binary files /dev/null and b/story-boards/starting-from-known-gene/genenetwork-home.png differ diff --git a/story-boards/starting-from-known-gene/genenetwork.png b/story-boards/starting-from-known-gene/genenetwork.png deleted file mode 100644 index 06c16f3..0000000 Binary files a/story-boards/starting-from-known-gene/genenetwork.png and /dev/null differ diff --git a/story-boards/starting-from-known-gene/generate.sh b/story-boards/starting-from-known-gene/generate.sh index 30d5279..d309ef8 100755 --- a/story-boards/starting-from-known-gene/generate.sh +++ b/story-boards/starting-from-known-gene/generate.sh @@ -1,3 +1,8 @@ #!/bin/bash -ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/" --out genenetwork.png +ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/" --out genenetwork-home.png +convert -extract 800x100+0+0 genenetwork-home.png global-search.png + +ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/gsearch?type=gene&terms=Brca2" --out global-search-gene.png --extract 800x300+0+0 + +ruby ../../scripts/screenshot.rb --url "https://genenetwork.org/show_trait?trait_id=1448542_at&dataset=HC_M2_0606_P" --out gene-aliases.png --extract 800x800+0+0 diff --git a/story-boards/starting-from-known-gene/global-search-gene.png b/story-boards/starting-from-known-gene/global-search-gene.png index 730e13e..f7f477b 100644 Binary files a/story-boards/starting-from-known-gene/global-search-gene.png and b/story-boards/starting-from-known-gene/global-search-gene.png differ diff --git a/story-boards/starting-from-known-gene/global-search.png b/story-boards/starting-from-known-gene/global-search.png new file mode 100644 index 0000000..b2cf1ef Binary files /dev/null and b/story-boards/starting-from-known-gene/global-search.png differ 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 38de598..3eaaafd 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 @@ -2,41 +2,30 @@ GeneNetwork contains data on thousands of experiments. How do you mine GN when you have the name of a gene? Start with [BRCA2](https://genenetwork.org/genes/BRCA2). -# Table of contents -1. [Global search](#gsearch) -1. [Gene aliases](#alias) -1. [Genewiki](#genewiki) -1. [TODO](#TODO) +## Use the search page -## Use the search page +The top bar of GeneNetwork shows a global search: -The top bar of GeneNetwork shows a global search. +[![Home page](./global-search.png "Global search")](https://genenetwork.org/) -![Home page](./genenetwork.png "The GeneNetwork HOME") - -We can look for the `Brca2` mouse gene: - -

- Global gene search -

+We can look for the `Brca2` mouse gene, resulting in +[![Global search](./global-search-gene.png "Global search gene")]() ## Find the right alias/name GeneNetwork knows about aliases. But sometimes you want to check what aliases there are in mouse. If you search for BRCA2 and click on a search result, for example for [1448542_at](http://genenetwork.org/show_trait?trait_id=1448542_at&dataset=HC_M2_0606_P), you get to the 'trait page' which shows the aliases: -

- Gene aliases -

+[![Gene aliases](./gene-aliases.png "Gene aliase")](https://genenetwork.org/show_trait?trait_id=1448542_at&dataset=HC_M2_0606_P) GeneNetwork ignores case by default. In a search use quotes to search case sensitive. For example, [BRCA2](https://www.wikidata.org/wiki/Q17853272) on wikidata.org refers to the human gene. The mouse gene is named [Brca2](https://www.wikidata.org/wiki/Q14864738). -## Find the GeneNetwork genewiki entry +## Find the GeneNetwork genewiki entry GeneNetwork maintains info on gene entries. For example for [BRCA2](http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2). -## TODO +## TODO * [ ] expand story line * [ ] global search is faulty, see gn-gemtext-threads/issues/genenetwork/global-search.gmi -- cgit v1.2.3