From 2ee6ad011e9c8c73e15dfe9d4f41c11e12c4e848 Mon Sep 17 00:00:00 2001
From: fynnkroeger <37335646+fynnkroeger@users.noreply.github.com>
Date: Thu, 28 Sep 2023 14:42:57 +0200
Subject: [PATCH] Uniprot docs (#285)
* add docs
* add to database page
* implement suggestions
---
docs/UniProt_download.md | 52 ++++++++++++++++++++++++++++++
ui/static/templates/databases.html | 4 +++
2 files changed, 56 insertions(+)
create mode 100644 docs/UniProt_download.md
diff --git a/docs/UniProt_download.md b/docs/UniProt_download.md
new file mode 100644
index 000000000..dfc9b9ca0
--- /dev/null
+++ b/docs/UniProt_download.md
@@ -0,0 +1,52 @@
+# UniProt usage in PROTzilla
+To make use of the UniProt integration in PROTzilla, tables with information on
+proteins need to be added to PROTzilla via the Databases page. Afterward, they
+can be used for Gene mapping if they contain a `Gene Names` or `Gene Names
+(primary)` column, or for adding UniProt data to a PROTzilla table.
+
+Frequently used tables can be found where PROTzilla is released, at
+https://github.com/cschlaffner/PROTzilla2/releases .
+By using the UniProt website at https://www.uniprot.org/uniprotkb?query= ,
+tables, that contain the proteins that interest you with the columns that you
+need, can be downloaded.
+
+
+### How to query UniProt
+
+In the sidebar on the left, you can choose if you want all proteins, or just
+the reviewed ones, as well as select proteins by species or other
+characteristics. If you are interested in characteristics that are not shown or
+want to choose a different organism, you can use the "Advanced" button in the
+search bar at the top. With the advanced search, you can build complex
+conditions for what proteins should be contained in the result out of pairs of
+field and value, such as "Taxonomy: Homo sapiens AND Reviewed: Yes". More
+information can be found at https://www.uniprot.org/help/filter_options
+The number of results is shown above the table that displays the first few
+results. The columns that are visible can be changed with the
+"Customize columns" button above the table. There is a vast selection of
+columns available.
+
+
+### Downloading from UniProt
+
+When you have selected the proteins that you want to download to be added to
+PROTzilla, you can click the "Download" button above the table. In the "Format"
+selector, you need to choose "TSV". If you select "Compressed: Yes", you will
+need to decompress the file before adding it to PROTzilla.
+
+In the "Customize columns" section, you need to choose the columns that you
+want to have available in PROTzilla. When you click the "Download" button at
+the bottom, a browser download will start. The download could take several
+minutes if you have selected more than 100,000 proteins or many columns. If you
+have selected more than 10,000,000 proteins, the file will be generated and you
+can download it later.
+
+
+### Adding to PROTzilla
+
+As a last step, the downloaded file needs to be added to PROTzilla. This is
+done via the databases page, which can be reached by clicking on the "Manage
+Databases" button on the main page. Then, you have to input a name and select
+the file for upload. After the "Add new database" button is clicked, the table
+is available for adding info and mapping genes, and is listed at the bottom of
+the tables page.
diff --git a/ui/static/templates/databases.html b/ui/static/templates/databases.html
index 3882a3b86..8fc96ead9 100644
--- a/ui/static/templates/databases.html
+++ b/ui/static/templates/databases.html
@@ -36,6 +36,10 @@
{% endif %}
+
+ To download a database, go to uniprot.org/uniprotkb. A tutorial is available in the PROTzilla documentation.
+