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khanspers committed Nov 22, 2024
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2 changes: 1 addition & 1 deletion stages/sig-cascade/index.html
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Expand Up @@ -38,7 +38,7 @@ <h1>
</h1>

<h2>Background</h2>
<p></p>
<p>A signaling cascade is a series of chemical reactions that occur within cells when in response to a stimulus, for example a ligand binding a receptor. The signal is transduced to the cell interior through second messengers which amplify the signal and transfer it to effector molecules, causing the cell to respond to the initial stimulus. Most signaling cascades are composed of series of events, in which one event triggers the next, in a linear way. Signaling cascades commonly result in effects on transcription factors, which in turn affect transcription of specific genes. In our pathway, the binding of Insulin to the Insulin receptor triggers the PI3K/Akt pathway, which leads to several downstream effects.</p>
<h2>Your Mission</h2>
<p>Draw the part of the pathway outlined in red below:</p>
<img src="40001_2024_1708_Fig2_HTML-cascade.jpg" width="500px">
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4 changes: 2 additions & 2 deletions stages/sig-phosphorylation/index.html
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Expand Up @@ -40,11 +40,11 @@ <h1>
<h2>Background</h2>

<p>Protein phosphorylation is a common post-translational modification of proteins, which involves the addition of a phosphate group to specific amino acids of a
protein by enzymes called kinases. The phosphorylation of proteins affects their activity, either activating or inactivating them, and is a common theme in signal transduction cascades. In the case of the Glucose-insulin signaling pathway, the binding of Insulin to the insulin receptor (INSR) causes conformational changes and autophosphorylion which activates the insulin receptor. The <b>Insulin receptor substrate</b> (IRS1) can then bind the insulin receptor and is subsequently phosphorylated by INSR, which activates the protein, thus transmitting the signal to downstream pathways. Although the pathway figure appears to show phosphorylation of INSR, the article text actually mentions IRS1: <i>"Insulin controls glucose metabolism and results in glucose uptake through the phosphorylation of insulin receptor substrate...."</i>, so we will model this phosphorylation. It is not uncommon that information in pathway figures in publications differ from the information in the article text, so it is important to read the article in full and cross-check all information.</p>
protein by enzymes called kinases. The phosphorylation of proteins affects their activity, either activating or inactivating them, and is a common theme in signal transduction cascades. In the case of the Glucose-insulin signaling pathway, the binding of Insulin to the insulin receptor (INSR) causes conformational changes and autophosphorylion which activates the insulin receptor. The Insulin receptor substrate (IRS1) can then bind the insulin receptor and is subsequently phosphorylated by INSR, which activates the protein, thus transmitting the signal to downstream pathways. Although the pathway figure appears to show phosphorylation of INSR, the article text actually mentions IRS1: <i>"Insulin controls glucose metabolism and results in glucose uptake through the phosphorylation of insulin receptor substrate...."</i>, so we will model this phosphorylation. It is not uncommon that information in pathway figures in publications differ from the information in the article text, so it is important to read the article in full and cross-check all information.</p>

<p>WikiPathways models allow for the addition of a number of <b>State</b> objects to any <b>DataNode</b>, which can be used to depict not only phosphorylation of specific
amino acid residues, but also other post-translational modifications. In addition to indicating that a protein is phosphorylated, we have developed a method for
adding specific site information to states on nodes in a way that is amenable to data mapping in tools like <a href="https://cytoscape.org/" target="_blank">Cytoscape</a>. The information is added as a <b>structured comment</b>. The process of protein phosphorylation by a kinase can be depicted in different ways, with varying degrees of detail. We will use a simplified style to indicate the phosphorylation of IRS1 by INSR usinf an arrow interaction directly from the INSR to IRS1 to indicate the activation caused by the phosphorylation, and a State node added to the IRS1 node.</p>
adding specific site information to states on nodes in a way that is amenable to data mapping in tools like <a href="https://cytoscape.org/" target="_blank">Cytoscape</a>. The information is added as a <b>structured comment</b>. The process of protein phosphorylation by a kinase can be depicted in different ways, with varying degrees of detail. We will use a simplified style to indicate the phosphorylation of IRS1 by INSR using an arrow interaction directly from the INSR to IRS1 to indicate the activation caused by the phosphorylation, and a State node added to the IRS1 node. For more detailed information on describing protein phosphorylation in pathways, see <a href="https://academy.wikipathways.org/stages/draw-protein-phosphorylation/" target="_blank">Protein Phosphorylation</a>.</p>
<!-- <img src="phosphorylation-process.png" width="50%">-->

<h2>Your Mission</h2>
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11 changes: 5 additions & 6 deletions stages/sig-start/index.html
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Expand Up @@ -41,20 +41,19 @@ <h1>

<h2>Background</h2>
<p>
This path desribes the process of authoring a pathway model from a published pathway figure. In this case, we will use a pathway figure from the <a href="https://pfocr.wikipathways.org/" target="_blank">Pathway Figure OCR</a> (PFOCR) project. Pathway Figure OCR is an open science project dedicated to extracting pathway information from the published literature. These instructions assume that you have everything you need to work with WikiPathways. [add links to setup and account creation]
</p>
<p>We will focus on a pathway figure below, describing Glucose-Insulin signaling, from a publication by <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10953212/">Mahmoudi et al</a>. To model this pathway, we will use the corresponding <a href="https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html">Pathway Figure OCR page for the figure</a> as well as the publication itself, and other resources. The first step, described below, is to access the genes and chemicals extracted by PFOCR to jump-start the pathway drawing process.</p>
<img src="40001_2024_1708_Fig2_HTML.jpg" width="500">
This path describes the process of authoring a pathway model from a published pathway figure. In this case, we will use a pathway figure from the <a href="https://pfocr.wikipathways.org/" target="_blank">Pathway Figure OCR</a> project. Pathway Figure OCR (PFOCR) is an open science project dedicated to extracting pathway information from the published literature. These instructions assume that you have everything you need to work with WikiPathways, including <a href="https://academy.wikipathways.org/stages/walk-install-pv/" target="_blank">PathVisio</a> and a <a href="https://academy.wikipathways.org/stages/wp-account/" target="_blank">WikiPathways account</a>.</p>
<p>We will focus on a pathway figure below, describing Glucose-Insulin signaling, from a publication by <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC10953212/">Mahmoudi et al</a>. To model this pathway, we will use the corresponding <a href="https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html">Pathway Figure OCR page</a> as well as the publication itself, and other resources. The first step, described below, is to access the genes and chemicals extracted by PFOCR to jump-start the pathway drawing process.</p>
<img src="40001_2024_1708_Fig2_HTML.jpg" width="600">
<h2>Getting Started</h2>
<ul>
<li>Launch PathVisio and load the human database and metabolite database.</li>
<li>Start a new pathway by selecting <b>File > New</b>. Close the <b>Pathway attributes</b> interface, and then reopen it by double-clicking on the <b>Pathway Information</b> area at the top left.</li>
<li>Enter "Glucose-insulin Signaling Pathway" as the pathway title and select "Homo saliens" as Organism.</li>
<li>Go to the <a href="https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html">Pathway Figure OCR webpage for the figure</a>.</li>
<li>Navigate to the <a href="https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html">Pathway Figure OCR webpage</a>.</li>
<li>Scroll down to <b>Gene mentions</b> and click the curved arrow symbol <img src="copyarrow.png" width="20"> and select <b>Copy DataNodes for PathVisio</b>.</li>
<li>In PathVisio, select <b>Edit > Paste</b> to paste the nodes. This will produce a set of stacked data nodes, that are already annotated with external references.</li>
<li>Repeat the process for the <b>Chemical mentions</b> on the PFOCR page. The metabolite nodes may end up in the same location as the gene product nodes; if so move the stack of nodes by click-and-drag while it is still selected.</li>
<li>The information from PFOCR is not always accurate, meaning words in the figure may be matched incorrecrly to gene and chemical annotations. Because of this, the data node annotation needs to be double-checked, and corrections made. In our case, some of the data nodes are false positives and should be deleted in PathVisio. Go ahead and delete the following nodes: MAP4K2, FAM20C, MAP4K5, GNAS, GNAL, BMS1, ACC (metabolite) and Glycogen.</li>
<li>The information from PFOCR is not always accurate, meaning words in the figure may be matched incorrectly to gene and chemical annotations. Because of this, the data node annotation needs to be double-checked, and corrections made. In our case, some of the data nodes are false positives and should be deleted in PathVisio. Go ahead and delete the following nodes: MAP4K2, FAM20C, MAP4K5, GNAS, GNAL, BMS1, ACC (metabolite) and Glycogen.</li>
</ul>
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14 changes: 6 additions & 8 deletions stages/sig-transcription/index.html
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Expand Up @@ -32,13 +32,12 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
<h1>
<a id="intro" class="anchor" href="#intro" aria-hidden="true">
<span aria-hidden="true" class="octicon octicon-link">
Signaling Pathway - Nucleus and Trannscription Factors
Signaling Pathway - Nucleus and Transcription Factors
</span>
</a>
</h1>

<h2>Background</h2>

<p>
</p>

Expand All @@ -50,22 +49,21 @@ <h2>Your Mission</h2>
<li>Launch PathVisio and open the dowloaded file or your draft pathway file via <b>File > Open</b>.</li>
<li>Perform the challenge tasks:</li>-->
<ul>
<li>Move FOXO1, SREBF1 and MLXIPL(official name for ChREBP) nodes into the center of the pathway, to the right of the signaling cascade.</li>
<li>Move FOXO1, SREBF1 and MLXIPL (official name for ChREBP) nodes into the center of the pathway, to the right of the signaling cascade.</li>
<li>Select the SREBF1 and MLXIPL nodes and stack them horizontally, then group them.</li>
<li>Add inhibition from the AKT1/2/3 group to FOXO1. To make it an arrow like in the figure, right-click on the interaction and select <b>Line type > Elbow</b>.</li>
<li>Add a pathway node for "Gluconeogenesis", and annotate it manually using "WP534" as the identifier and "WikiPathways" as the database.</li>
<li>Add another pathway node for "De novo lipigenesis". Since there is no pathway model at WikiPathways describing this process, leave the identifier and database empty.</li>
<li>Add <b>arrow</b> interaction from FOXO1 to the Gluconeogenesis node.</li>
<li>Add arrow from the SREBP1/MLXIPL group to the De novo lipogenesis node.</li>
<li>Select the <b>Nucleus</b> object from the <b>Objects</b> panel or the toolbar.</li>
<li>Click on the canvas to place the object.</li>
<li>Click on the canvas to place the nucleus near the three transcription factor nodes.</li>
<li>With the Nucleus object selected, use the yellow resize targets to change the size of the object to fit the FOXO1, SREBP1 and MLXIPL nodes.</li>
<li>With the cell object selected, click and drag anywhere on the object outline to position it over the entire catalysis reaction.</li>
<li>Select the Nucleus object and in the <p>Properties</p> panel, type in "Nucleus" for <b>Text Label</b>.</li>
<li>Select the Nucleus object and in the <b>Properties</b> panel, type in "Nucleus" for <b>Text Label</b>.</li>
<li>Under <b>Vertical Alignment</b>, select "Bottom".</li>
</ul>
<li>When you have completed the challenge, save your work as a GPML file under <b>File > Save As</b>.</li>
<li>Drag-and-drop the GPML file below to check if it is correct.</li>
<li>When you have completed the challenge, save your work as a GPML file under <b>File > Save As</b>.</li>
<li>Drag-and-drop the GPML file below to check if it is correct.</li>
</ul>

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11 changes: 6 additions & 5 deletions stages/sig-transport/index.html
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Expand Up @@ -39,6 +39,7 @@ <h1>

<h2>Background</h2>
<p>
The first step in this pathway is two-fold; the binding of Insulin to the Insulin receptor and the transport of Glucose into the cell aided by the glucose transporter SLC2A2 (GLUT2). In the figure, the receptor are illustrated by graphical objects that are perfectly interpretable by the human brain, but since they are not labeled, they can't be interepted/found by the OCR method that was used to extract information from this pathway. We will need to add data nodes for the receptor and the transporter.
</p>

<h2>Your Mission</h2>
Expand All @@ -47,18 +48,18 @@ <h2>Your Mission</h2>
<ul>
<!-- <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/draw-transport-start.gpml">draw-transport-start.gpml</a>.</li>
<li>Launch PathVisio and open the dowloaded file via <b>File > Open</b>.</li>-->
<li>Start with the draft pathway you saved in the previous step. Select all data nodes and moving them down a bit to create space.</li>
<li>Start with the draft pathway you saved in the previous step. Select all data nodes and move them down a bit to create space.</li>
<li>Add a gene product node for the Insulin receptor (INSR).</li>
<li>Move the Insulin node (metabolite) towards the top, and connect it with the INSR node using a <b>mim-binding</b> arrow, to indicate the binding of Insulin to the insulin receptor.</li>
<li>The label for the Insulin node is blank, so we need to update the label (ChEBI ID 5931) "Insulin.</li>
<li>Move the Insulin node towards the top, and connect it with the INSR node using a <b>mim-binding</b> arrow, to indicate the binding of Insulin to the insulin receptor.</li>
<li>Add a gene product node for the glucose transporter SLC2A2 and position it to the right of INSR.</li>
<li>There are two glucose nodes. Position them vertically aligned, above and below the SLC2A2 node, offset to the right.</li>
<li>Select the <b>arrow</b> interaction from the <b>Basic interactions</b> panel or the toolbar and use it to connect the two <b>glucose</b> nodes.</li>
<li>Right-click on the interaction and add an anchor, or select the conversion interaction and then use the keyboard shortcut <b>Ctrl+R</b> (<b>Command+R</b> on Mac), to add the anchor.</li>
<li>Select the <b>mim-catalysis</b> interaction from the <b>MIM interactions</b> panel and use it to connect the <b>SLC2A2</b> node to the anchor point on the conversion arrow, indicating that the transporter controls the transport of glucose into the cell.</li>
<li>Save your work as a GPML file under <b>File > Save As</b>.</li>
<li>Drag-and-drop the GPML file below to check if it is correct.</li>
</ul>
<li>Save your work as a GPML file under <b>File > Save As</b>.</li>
<li>Drag-and-drop the GPML file below to check if it is correct.</li>

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