Help:Tutorial:Step 2 v2
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| + | [[:Help:Tutorial:Step_3_v2|Next step]] | [[:Help:Tutorial|Index]] | ||
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| - | {{#ev:youtube| | + | = Creating a new pathway = |
| + | |||
| + | This step includes several aspects of pathway creation, from creating a pathway at WikiPathways, launching the Applet Editor, adding data nodes, interactions and annotations. | ||
| + | <!-- Uncomment this after mediawiki upgrade | ||
| + | {{#ev:youtube|N7cGHJ6HdGU|700|left|Create pathway, part1}} --> | ||
== Create a new pathway == | == Create a new pathway == | ||
| - | Open a new browser window or tab, go to the WikiPathways main page and click the image under the header ''Create'' | + | Open a new browser window or tab, go to the WikiPathways main page and click the image under the header '''Create''' in the left side panel. Enter ''Demo_yourname'' under the "Pathway name" field and select "Homo sapiens" in the species menu. Now click the '''Create pathway''' button. |
| - | After clicking the button, a new | + | After clicking the button, a link to the new Pathway Page will open. Open the page and to start the editor, click the '''Launch Editor''' button under the blank pathway diagram. |
| - | + | You can now start drawing your pathway. | |
== Adding initial gene products and metabolites == | == Adding initial gene products and metabolites == | ||
| - | For the purposes of this tutorial, we will use the Statin pathway as our example. On a WikiPathways pathway, all biological entities with an annotation are stored as a | + | For the purposes of this tutorial, we will use the Statin pathway as our example. We will start by adding a data node to the pathway. On a WikiPathways pathway, all biological entities with an annotation are stored as a data node. A data node can have different types, in this case, we will use the type Metabolite. |
| - | + | * To start, click the drop-down next to the '''GENE''' button and select '''Metabolite'''. Place the metabolite on the drawing are by dragging and dropping it. | |
| + | * To annotate the node, double-click the metabolite to bring up the '''DataNode properties''' interface. In the '''Annotation''' tab, type in "3-hydroxy-3-methylglutaryl-coA" and click '''Search'''. | ||
| - | + | Note that you can also manually fill in identifier and data source either in the '''DataNode properties''' interface or in the '''Properties''' tab in the right-side panel. | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | * In the search results, select the node with the HMDB identifier "HMDB01375". Click '''OK'''. | |
| - | + | * Back in the '''DataNode properties''' window, you can alter the text label that will be displayed on the metabolite. In this case, change it to "HMG-CoA". Click '''OK''' to save. | |
| - | + | ||
| - | + | Note that the text in the text label field will be displayed on the pathway and doesn't affect the annotation. | |
| + | |||
| + | * Repeat the steps above and add another metabolite node for "Mevalonate". Place it under the HMG-CoA node. | ||
| + | |||
| + | After annotating a data node, you check whether it's correctly annotated by selecting the data node and. Annotation info should appear in the '''Backpage''' tab of the side panel. | ||
| + | |||
| + | {{TutorialHint|Sometimes a gene symbol may not be found via the search feature. This is because some genes has two synonymous names, but only one is stored in the internal database. In this case, the data node has to be manually annotated.}} | ||
== Add interactions == | == Add interactions == | ||
Next, we need to connect the two metabolites: | Next, we need to connect the two metabolites: | ||
| - | + | * In the drop-down next to the '''Interaction''' button, select '''Conversion''' from the '''MIM interactions''' section. Place the interaction on the drawing area. | |
| - | + | * To attach the interaction, click on the non-arrow end of the interaction to select it, and drag it towards the HMG-CoA node. Red link anchors on the node will become visible as you drag the interaction towards it. Hover over a snap target to select it; it will be highlighted in green when selected. Simply let go of the interaction when you see the target highlight, and the interaction will attach. | |
| - | + | ||
| - | + | Note that you can release an interaction from it's link target by moving the interaction end away from the link anchor. | |
| + | |||
| + | * Repeat the process to attach the arrow-end of the interaction to Mevalonate. | ||
| + | * Once the two nodes are connected, you can move them by clicking and dragging to adjust the alignment and layout. | ||
| + | |||
| + | {{TutorialHint|It's good habit to connect the lines in your pathway wherever you can. It makes it easier to change the layout of the pathway in the future, because when you move an object, the connected lines will stick to it. Another advantage of defining connections is that it enables conversion of the pathway to graph format. When the interactions between the entities in the pathway are explicitly defined, this information can be used for computational purposes. For example, the pathway can be converted to a Cytoscape network to perform various graph analysis algorithms (see http://www.cytoscape.org).}} | ||
== Add enzymatic reaction == | == Add enzymatic reaction == | ||
We can now add the enzyme that converts HMG-CoA to Mevalonate, HMGCR: | We can now add the enzyme that converts HMG-CoA to Mevalonate, HMGCR: | ||
| - | + | * Add another data node of the GeneProduct and annotate it as "HMGCR". | |
| - | + | * Add an interaction of type '''Catalysis''', under '''MIM interactions'''. | |
| - | + | * Connect the start (plain) end of the catalysis to the left short-end of HMGCR. | |
The catalysis interaction works on the existing interaction between HMG-CoA and Mevalonate. To connect the catalysis interaction to this interaction, we first need to add an anchor to the conversion interaction. | The catalysis interaction works on the existing interaction between HMG-CoA and Mevalonate. To connect the catalysis interaction to this interaction, we first need to add an anchor to the conversion interaction. | ||
| - | + | * To add an anchor, right-click on the conversion interaction and select '''Add anchor'''. You can adjust the position of the anchor by click and drag. | |
| - | + | * Attach the catalysis interaction to the anchor. | |
== Add inhibition of the catalysis by Statin == | == Add inhibition of the catalysis by Statin == | ||
We can now add the inhibition of the catalysis by Statin. | We can now add the inhibition of the catalysis by Statin. | ||
| - | + | * Add another metabolite data node. In the '''DataNode properties''' interface, search for Statin. There will be multiple results, choose "Pravastatin". For simplicity, change the text label to "Statin". | |
| - | + | * Now, add an interaction of type '''Inhibition''' (under '''MIM interactions''') and connect the plain end to the Statin node. | |
| - | + | * Add an anchor on the HMGCR catalysis interaction. | |
| - | + | * Connect the inhibition end of the new interaction to the anchor. | |
| - | + | * To make the interactions easier to read, change the style of the inhibition interaction to an elbow. You can do this by right-clicking the interaction and selecting '''Line type > elbow'''. | |
== Changing the color and style of interactions == | == Changing the color and style of interactions == | ||
Inhibitions are often depicted as red in pathway illustrations, so in keeping with this convention, let's change the color of the inhibition to red: | Inhibitions are often depicted as red in pathway illustrations, so in keeping with this convention, let's change the color of the inhibition to red: | ||
| - | + | * Select the inhibition interaction. | |
| - | + | * In the right-side '''Properties''' panel, change the color to red. | |
| + | |||
| + | == Saving changes == | ||
| + | |||
| + | * To save the pathway, go to '''Plugins -> WikiPathways -> Update'''. You will be asked to provide a description of your changes. | ||
| + | * Once the pathway is saved at WikiPathways, the Pathway Page will be updated with your changes. | ||
| - | + | {{TutorialHint|You can also save the pathway locally on your hard drive, under '''File -> Save As'''. Saving a pathway locally once in a while is usually a good habit to prevent losing your changes when an error occurs.}} | |
| - | + | [[:Help:Tutorial:Step_3_v2|Next step]] | [[:Help:Tutorial|Index]] | |
| - | + | ||
Current revision
Creating a new pathway
This step includes several aspects of pathway creation, from creating a pathway at WikiPathways, launching the Applet Editor, adding data nodes, interactions and annotations.
Create a new pathway
Open a new browser window or tab, go to the WikiPathways main page and click the image under the header Create in the left side panel. Enter Demo_yourname under the "Pathway name" field and select "Homo sapiens" in the species menu. Now click the Create pathway button.
After clicking the button, a link to the new Pathway Page will open. Open the page and to start the editor, click the Launch Editor button under the blank pathway diagram.
You can now start drawing your pathway.
Adding initial gene products and metabolites
For the purposes of this tutorial, we will use the Statin pathway as our example. We will start by adding a data node to the pathway. On a WikiPathways pathway, all biological entities with an annotation are stored as a data node. A data node can have different types, in this case, we will use the type Metabolite.
- To start, click the drop-down next to the GENE button and select Metabolite. Place the metabolite on the drawing are by dragging and dropping it.
- To annotate the node, double-click the metabolite to bring up the DataNode properties interface. In the Annotation tab, type in "3-hydroxy-3-methylglutaryl-coA" and click Search.
Note that you can also manually fill in identifier and data source either in the DataNode properties interface or in the Properties tab in the right-side panel.
- In the search results, select the node with the HMDB identifier "HMDB01375". Click OK.
- Back in the DataNode properties window, you can alter the text label that will be displayed on the metabolite. In this case, change it to "HMG-CoA". Click OK to save.
Note that the text in the text label field will be displayed on the pathway and doesn't affect the annotation.
- Repeat the steps above and add another metabolite node for "Mevalonate". Place it under the HMG-CoA node.
After annotating a data node, you check whether it's correctly annotated by selecting the data node and. Annotation info should appear in the Backpage tab of the side panel.
Note: Sometimes a gene symbol may not be found via the search feature. This is because some genes has two synonymous names, but only one is stored in the internal database. In this case, the data node has to be manually annotated.
Add interactions
Next, we need to connect the two metabolites:
- In the drop-down next to the Interaction button, select Conversion from the MIM interactions section. Place the interaction on the drawing area.
- To attach the interaction, click on the non-arrow end of the interaction to select it, and drag it towards the HMG-CoA node. Red link anchors on the node will become visible as you drag the interaction towards it. Hover over a snap target to select it; it will be highlighted in green when selected. Simply let go of the interaction when you see the target highlight, and the interaction will attach.
Note that you can release an interaction from it's link target by moving the interaction end away from the link anchor.
- Repeat the process to attach the arrow-end of the interaction to Mevalonate.
- Once the two nodes are connected, you can move them by clicking and dragging to adjust the alignment and layout.
Note: It's good habit to connect the lines in your pathway wherever you can. It makes it easier to change the layout of the pathway in the future, because when you move an object, the connected lines will stick to it. Another advantage of defining connections is that it enables conversion of the pathway to graph format. When the interactions between the entities in the pathway are explicitly defined, this information can be used for computational purposes. For example, the pathway can be converted to a Cytoscape network to perform various graph analysis algorithms (see http://www.cytoscape.org).
Add enzymatic reaction
We can now add the enzyme that converts HMG-CoA to Mevalonate, HMGCR:
- Add another data node of the GeneProduct and annotate it as "HMGCR".
- Add an interaction of type Catalysis, under MIM interactions.
- Connect the start (plain) end of the catalysis to the left short-end of HMGCR.
The catalysis interaction works on the existing interaction between HMG-CoA and Mevalonate. To connect the catalysis interaction to this interaction, we first need to add an anchor to the conversion interaction.
- To add an anchor, right-click on the conversion interaction and select Add anchor. You can adjust the position of the anchor by click and drag.
- Attach the catalysis interaction to the anchor.
Add inhibition of the catalysis by Statin
We can now add the inhibition of the catalysis by Statin.
- Add another metabolite data node. In the DataNode properties interface, search for Statin. There will be multiple results, choose "Pravastatin". For simplicity, change the text label to "Statin".
- Now, add an interaction of type Inhibition (under MIM interactions) and connect the plain end to the Statin node.
- Add an anchor on the HMGCR catalysis interaction.
- Connect the inhibition end of the new interaction to the anchor.
- To make the interactions easier to read, change the style of the inhibition interaction to an elbow. You can do this by right-clicking the interaction and selecting Line type > elbow.
Changing the color and style of interactions
Inhibitions are often depicted as red in pathway illustrations, so in keeping with this convention, let's change the color of the inhibition to red:
- Select the inhibition interaction.
- In the right-side Properties panel, change the color to red.
Saving changes
- To save the pathway, go to Plugins -> WikiPathways -> Update. You will be asked to provide a description of your changes.
- Once the pathway is saved at WikiPathways, the Pathway Page will be updated with your changes.
Note: You can also save the pathway locally on your hard drive, under File -> Save As. Saving a pathway locally once in a while is usually a good habit to prevent losing your changes when an error occurs.
