From 37701cd7d5c45d8caef0c96639d3f3f94b91ef17 Mon Sep 17 00:00:00 2001 From: khanspers Date: Thu, 3 Aug 2023 12:32:58 -0700 Subject: [PATCH] updated starter pathway titles, update instructions, update titles for stages --- ...{WP3966.gpml => draw-catalysis-start.gpml} | 0 data/{WP3910.gpml => draw-complex-start.gpml} | 0 data/{WP3905.gpml => met-1-first-start.gpml} | 0 ...{WP3909.gpml => met-1-indirect-start.gpml} | 0 data/{WP3907.gpml => met-1-last-start.gpml} | 0 data/{WP3908.gpml => met-1-second-start.gpml} | 0 stages/draw-catalysis/index.html | 7 +-- stages/draw-complex/index.html | 6 +-- stages/draw-conversion/index.html | 21 ++++----- stages/draw-geneproduct/index.html | 4 +- stages/draw-metabolite/index.html | 4 +- stages/met-1-first/index.html | 42 ++---------------- stages/met-1-indirect/index.html | 40 ++--------------- stages/met-1-last/index.html | 42 ++---------------- stages/met-1-second/index.html | 43 ++----------------- stages/walk-install-pv/index.html | 6 +-- stages/wp-add-literature/index.html | 2 +- 17 files changed, 41 insertions(+), 176 deletions(-) rename data/{WP3966.gpml => draw-catalysis-start.gpml} (100%) rename data/{WP3910.gpml => draw-complex-start.gpml} (100%) rename data/{WP3905.gpml => met-1-first-start.gpml} (100%) rename data/{WP3909.gpml => met-1-indirect-start.gpml} (100%) rename data/{WP3907.gpml => met-1-last-start.gpml} (100%) rename data/{WP3908.gpml => met-1-second-start.gpml} (100%) diff --git a/data/WP3966.gpml b/data/draw-catalysis-start.gpml similarity index 100% rename from data/WP3966.gpml rename to data/draw-catalysis-start.gpml diff --git a/data/WP3910.gpml b/data/draw-complex-start.gpml similarity index 100% rename from data/WP3910.gpml rename to data/draw-complex-start.gpml diff --git a/data/WP3905.gpml b/data/met-1-first-start.gpml similarity index 100% rename from data/WP3905.gpml rename to data/met-1-first-start.gpml diff --git a/data/WP3909.gpml b/data/met-1-indirect-start.gpml similarity index 100% rename from data/WP3909.gpml rename to data/met-1-indirect-start.gpml diff --git a/data/WP3907.gpml b/data/met-1-last-start.gpml similarity index 100% rename from data/WP3907.gpml rename to data/met-1-last-start.gpml diff --git a/data/WP3908.gpml b/data/met-1-second-start.gpml similarity index 100% rename from data/WP3908.gpml rename to data/met-1-second-start.gpml diff --git a/stages/draw-catalysis/index.html b/stages/draw-catalysis/index.html index 782c6bc..47f5df4 100644 --- a/stages/draw-catalysis/index.html +++ b/stages/draw-catalysis/index.html @@ -32,7 +32,7 @@

Organized training challenges for new WikiPathways authors

@@ -46,6 +46,7 @@

Background

Your Mission

Draw the catalysis reaction depicted in this figure:

+

This reaction is described in many publications. For our example, we will use the publication from Strushkevich et al. which includes the following sentence:

"The first step in steroid hormone biosynthesis is the conversion of cholesterol to pregnenolone and isocaproic aldehyde by mitochondrial CYP11A1."
@@ -60,7 +61,7 @@

Your Mission


diff --git a/stages/draw-complex/index.html b/stages/draw-complex/index.html index e4fdb53..3abfef9 100644 --- a/stages/draw-complex/index.html +++ b/stages/draw-complex/index.html @@ -32,7 +32,7 @@

Organized training challenges for new WikiPathways authors

@@ -50,14 +50,14 @@

Your Mission


diff --git a/stages/draw-conversion/index.html b/stages/draw-conversion/index.html index 8b2fa95..263a786 100644 --- a/stages/draw-conversion/index.html +++ b/stages/draw-conversion/index.html @@ -32,7 +32,7 @@

Organized training challenges for new WikiPathways authors

@@ -41,7 +41,7 @@

Background

The conversion of one metabolite into another comprises the fundamental biological process of metabolism. Often catalyzed by enzymes and chained together in a series, each conversion reaction involves a change in the chemical structure of a metabolite or small molecule. - Conversion reactions are thus drawn as two metabolites and a mim-conversion interaction, pointing from the subtrate to the product. MIM + Conversion reactions are thus drawn as two metabolites and a mim-conversion interaction, pointing from the substrate to the product. MIM is a diagram convention that includes specific notations for interactions, which are included in WikiPathways. Since their meaning is specific, they should be used only in specific circumstances, as in this case, for a conversion between two metabolites.

Note that for the example below, we are only modeling part of the full reaction; we are excluding the enzyme that catalyses the reaction. The next step will show @@ -56,22 +56,23 @@

Your Mission

  • Launch PathVisio and select File > New to start a new pathway. Close the Pathway attributes dialog.
  • In the upper left of the canvas, the Pathway Information area will be displayed, and will say "Title: New Pathway". Select this by clicking on it, and in the Properties tab select "Homo sapiens" in the Species menu.
  • Select Metabolite from the Data Node palette in the Objects tab.
    • -
  • Click on the canvas to place the node.
    • -
  • Double-click on the node to open its properties.
    • +
  • Click on the canvas to place the node.
    • +
  • Double-click on the node to open its properties.
  • Search for “glucose”; Choose any of the entries that just say “glucose”; Click OK to select the identifier, and then click OK again to close the node properties window.
    • -
  • Repeat these steps to make the “glucose 6-phosphate” metabolite node. Note that searching for exact matches of metabolite names can be tricky, as some databases +
  • Repeat these steps to add the “glucose 6-phosphate” metabolite node. Note that searching for exact matches of metabolite names can be tricky, as some databases might use the name "glucose 6-phosphate", while others use "glucose-6-phosphate".
  • Select the mim-conversion arrow from the MIM interactions palette in the Objects tab:
    • -
  • Click anywhere on the canvas to create the interaction.
    • -
  • Drag each end of the interaction over a target area on each node (highlighted in green on hover); Note source vs target. The video below shows how to attach the ends of the interaction to the nodes.
    +
  • Click anywhere on the canvas to create the interaction.
    • +
  • Drag each end of the interaction over a target area on each node (highlighted in green on hover) to connect the interaction to the node, noting source vs target. The video below shows how to attach the ends of the interaction to the nodes.

    • -
  • (Optional) Align nodes using toolbar actions. To align nodes, select them both, then click the Align horizontal centers button +
    +
  • (Optional) Align nodes using toolbar actions. To align nodes, select them both, then click the Align horizontal centers button from the toolbar.
  • Done!
    • -
  • Save your work as a GPML file under File > Save As.
    • -
  • Drag-and-drop the GPML file below to submit.
    • +
  • Save your work as a GPML file under File > Save As.
    • +
  • Drag-and-drop the GPML file below to check if it is correct.
    • diff --git a/stages/draw-geneproduct/index.html b/stages/draw-geneproduct/index.html index 90e9153..b1addf0 100644 --- a/stages/draw-geneproduct/index.html +++ b/stages/draw-geneproduct/index.html @@ -53,12 +53,12 @@

    Your Mission

    by clicking on it, and in the Properties tab select "Homo sapiens" in the Species menu.
  • Select GeneProduct from the Data Node palette in the Objects tab.
  • Click on the canvas to place the node.
    • -
  • Double-click on the node to open its properties.
    • +
  • Double-click on the node to open the DataNode properties dialog.
  • Search for “ACO2”; Choose any of the entries that just say “ACO2”. In terms of choosing which identifier system to use, we recommend the following priority order: Ensembl, Entrez, other systems.
  • Click OK to select the identifier, and then click OK again to close the node properties window.
  • Done!
  • Save your work as a GPML file under File > Save As.
    • -
  • Drag-and-drop the GPML file below to submit.
    • +
  • Drag-and-drop the GPML file below to check if it is correct.
    • diff --git a/stages/draw-metabolite/index.html b/stages/draw-metabolite/index.html index 3615ca5..6b53e86 100644 --- a/stages/draw-metabolite/index.html +++ b/stages/draw-metabolite/index.html @@ -48,7 +48,7 @@

    Your Mission

    diff --git a/stages/met-1-first/index.html b/stages/met-1-first/index.html index ee8d414..9e469fa 100644 --- a/stages/met-1-first/index.html +++ b/stages/met-1-first/index.html @@ -32,7 +32,7 @@

    Organized training challenges for new WikiPathways authors

    @@ -40,7 +40,7 @@

    Background

    Because of the importance of cholesterol, all animal cells are able to synthesize it. The cholesterol biosynthesis starts - with Acetyl-CoA.

    + with the cataluzed conversion of Acetyl-CoA into HMG-CoA.

    Your Mission

    Complete the first step of the cholesterol biosynthesis pathway, the conversion of Acetyl-CoA to HMG-CoA, catalyzed by @@ -49,7 +49,7 @@

    Your Mission



    - - - - - -
    diff --git a/stages/met-1-indirect/index.html b/stages/met-1-indirect/index.html index 0cb7a7d..99abd41 100644 --- a/stages/met-1-indirect/index.html +++ b/stages/met-1-indirect/index.html @@ -32,7 +32,7 @@

    Organized training challenges for new WikiPathways authors

    @@ -51,7 +51,7 @@

    Your Mission



    - - - - - -
    diff --git a/stages/met-1-last/index.html b/stages/met-1-last/index.html index fe6770d..9e49078 100644 --- a/stages/met-1-last/index.html +++ b/stages/met-1-last/index.html @@ -32,7 +32,7 @@

    Organized training challenges for new WikiPathways authors

    @@ -50,7 +50,7 @@

    Your Mission



      -
    • Download the starter pathway here: WP3907.
      • +
    • Download the starter pathway here: met-1-last-start.gpml.
    • Launch PathVisio and open the dowloaded file via File > Open.

        • Add the metabolite node

        @@ -79,43 +79,9 @@

        Add a pathway name

      • Update the pathway title in the Title field. Briefly, the pathway name should be in English, and should be sentence case.
    • Save your work as a GPML file under File > Save As.
      • -
    • Drag-and-drop the GPML file below to submit.
      • +
    • Drag-and-drop the GPML file below to check if it is correct.
    - - - - - - - +
    diff --git a/stages/met-1-second/index.html b/stages/met-1-second/index.html index a9749ea..8b2a3f9 100644 --- a/stages/met-1-second/index.html +++ b/stages/met-1-second/index.html @@ -32,15 +32,14 @@

    Organized training challenges for new WikiPathways authors

    Background

    -

    Cholesterol biosynthesis is composed of - a series of enzymatically catalyzed reactions. Each step is catalyzed by one or more enzymes.

    +

    Cholesterol biosynthesis is composed of a series of enzymatically catalyzed reactions. Each step is catalyzed by one or more enzymes.

    Your Mission

    Complete the second step of the Cholesterol biosynthesis pathway, the conversion of HMG-CoA to Mevalonic acid, catalyzed by @@ -49,7 +48,7 @@

    Your Mission



      -
    • Download the starter pathway here: WP3908.
      • +
    • Download the starter pathway here: met-1-second-start.gpml.
    • Launch PathVisio and open the dowloaded file via File > Open.

        • Add the metabolite

        @@ -78,42 +77,8 @@

        Add and connect the catalysis arrow

      • Done!
    • Save your work as a GPML file under File > Save As.
      • -
    • Drag-and-drop the GPML file below to submit.
      • +
    • Drag-and-drop the GPML file below to check if it is correct.
    - - - - - -
    diff --git a/stages/walk-install-pv/index.html b/stages/walk-install-pv/index.html index 7084fa5..59c9ba7 100644 --- a/stages/walk-install-pv/index.html +++ b/stages/walk-install-pv/index.html @@ -45,11 +45,11 @@

    Install PathVisio

    Installation instructions for your operating system.

    Setup a mapping database

    -
  • Launch PathVisio:
    • +
  • Launch PathVisio:
    • Windows: start PathVisio by double-clicking the pathvisio.bat file.
      • -
    • MacOSX / Linux: start PathVisio by running pathvisio.sh or double-click the pathvisio.jar file.
      • -
    +
  • MacOS / Linux: start PathVisio by running pathvisio.sh or double-click the pathvisio.jar file.
    • +
  • In PathVisio, go to Plugins > Plugin manager. Find the BridgeDbConfig plugin from the list of plugins on the left side.
  • Click the Install button to install.
  • Select Data > Identifier mapping setup and click Add. In the interface select BridgeRest webservice in the left sidebar.
    • diff --git a/stages/wp-add-literature/index.html b/stages/wp-add-literature/index.html index 0848183..af16840 100644 --- a/stages/wp-add-literature/index.html +++ b/stages/wp-add-literature/index.html @@ -33,7 +33,7 @@

    Organized training challenges for new WikiPathways authors