Help:Editing Pathways

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In addition to editing the text fields on a given [[:Help:Viewing Pathways|''Pathway Page'']], this wiki also supports the ability to edit the pathway itself! Click on ''Edit pathway'' on any ''Pathway Page'' and a embedded version of the [http://www.pathvisio.org PathVisio] program will open with the current pathway loaded. You can then add, edit or delete content from the pathway. When you save, updated versions of the images, controlled text, and data files are generated and are immediately available.  
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'''The main editor for WikiPathways is a webstart version of PathVisio. You can also edit data node annotation and style directly at WikiPathways using the Quick Edit feature.'''
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Try it out in the [[:Pathway:Human:Sandbox|Sandbox pathway]]!
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<!--
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{{#ev:youtube|tYD9JxILxv8|700|left|Intro to Editing Video}}
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__NOTOC__
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= Editing in PathVisio Webstart =
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== Editing the pathway image ==
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Each pathway page at WikiPathways has an '''Launch Editor''' button, which launches [http://www.pathvisio.org PathVisio webstart] with the pathway in question loaded. This utilizes the [[:Help:WPClientPluginCuration|WikiPathways Client plugin]].  
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Pathway editing for WikiPathways is done in an embedded version of the [http://wiki.bigcat.unimaas.nl/pathvisio/Main_Page PathVisio] program. PathVisio supports a number of common drawing tools, as well as an interface for linking objects on pathways to an underlying gene database. For detailed instructions on how to use the PathVisio program please refer to the [http://www.pathvisio.org/wiki/PathVisioHelp PathVisio documentation] and [http://www.pathvisio.org/wiki/PathVisioFaq PathVisio FAQ].
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In addition to the drawing features described for the PathVisio webstart program, the WikiPathways embedded editor has some additional features.
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==== Adding, selecting, sizing and moving objects ====
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* Click the '''Launch Editor''' button on any '''Pathway Page''' to open the [http://www.pathvisio.org PathVisio] program with the current pathway loaded. You can add, edit or delete content from the pathway and when you save, updated versions of the images, controlled text, and data files are generated and are immediately available. For instructions on basic editing features please refer to [http://www.pathvisio.org/documentation/editing-and-viewing-pathways/ PathVisio documentation].  
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For instructions on basic editing features please refer to [http://www.pathvisio.org/wiki/PathVisioHelp PathVisio documentation].
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==== Grouping objects ====
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* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.  
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To group objects, first select the objects to be grouped by click and drag. Grouping the objects can be done in two ways: either right-click and select Group from the context menu or click ^G on your keyboard.
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The display of grouped objects does not change once the objects are grouped. When the cursor is placed over a group, a boxed outline will appear highlighting the grouped objects. [http://www.youtube.com/watch?v=mAultpJCLJk&fmt=18 Watch video].
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==== Representing complexes ====
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* You can also browse WikiPathways and open and edit any pathway from within PathVisio, as well as create new pathways. For more details, see [[:Help:WPClientPluginCuration|Using the WikiPathways Client plugin]].
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To create a complex, first select the objects in the complex by click and drag. Creating the complex can be done in two ways: either right-click and select Group from the context menu or click ^P on your keyboard.
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= Editing using Quick Edit =
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The display of a complex includes a boxed outline around the group. [http://www.youtube.com/watch?v=A7ryJwV4Y00&fmt=18 Watch video].
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We have a new, quick way to edit data node annotations and styles. When logged in, the '''Quick Edit''' button is located at the bottom center of the pathway view. Clicking the '''Quick Edit''' button opens the editor:
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==== Selecting grouped objects and complexes ====
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[[Image:QuickEdit.png]]
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Grouped objects and complexes can be selected as a group, or as individual objects. To select the group as a whole (all group objects), click anywhere in the boxed outline surrounding the group. For complexes, this outline will be permanently visible, and for groups this outline will be visible only when the cursor is placed over the group. To select an individual object in a group, click the object directly.
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{|class="prettytable"
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|-
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!Selecting whole group
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|-
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|[[Image:GroupSelection.png]]
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|}
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{|class="prettytable"
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|-
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!Selecting single grouped object
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|-
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|[[Image:SingleGroupSelection.png]]
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|}
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==== Adding connectors between objects ====
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=== Editing data node annotation ===
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Connecting line objects with gene and metabolite objects on pathways are important for properly storing the biological interactions that the pathway represents. To connect the end of a line to a gene or metabolite, select the end point of the line and drag it close to the object you wish to connect it to. A set of anchor points will appear on the outline of the object. Drag the end of the line over any of these anchor points until the anchor point turns green, then let go of the line end. This will connect the end of the line to the anchor point on the object.
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* Open Quick Edit.
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{|class="prettytable"
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* Select any data node to display its current annotation in the annotation tab.
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|-
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* To search for a new identifier, type in a gene name or label in the '''Search by name''' field and click the green '''Search''' button. Results are displayed in a separate results panel. Select an identifier from the list of results to assign it to the node.
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!Adding connectors
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* To change only the data node type or data source, simply select from the drop-down lists.
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|-
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* To manually change the label or identifier, simply type directly in the corresponding field.
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|[[Image:Connectors.png]]
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* Click the '''Save & Close''' button to save and exit Quick Edit.
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|}
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<p>Objects that have anchor points that can be connected to lines are data nodes, metabolites, labels and graphical objects. Anchor points can also be added to lines (from the right-click menu), after which other lines can be connected to it.</p> 
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==== Creating curved, elbowed lines and composite lines ====
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=== Editing data node style ===
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For layout reasons and to properly represent biological interactions, curved or elbowed lines are sometimes ideal. To create a curved or elbowed line, first create a new line by selecting the line object from the tool bar and dropping it on the canvas. Right-click on the line and under Line Type, select either Curved or Elbow. The Curved option will produce a curved line with smooth edges, whereas the Elbow option will create a curved line with 90 degree edges. To position the line, attach the end points to the desired objects as described above. The shape of the curved line will automatically adjust to fit the layout of the objects you are connecting. You can also change the shape of the line manually by dragging the way points (blue diamonds) on the line.
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* Open Quick Edit.
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{|class="prettytable"
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* Select a data node and click the '''Properties''' tab in Quick Edit.
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|-
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* Use the color chooser to change the border and label color of the node, or use the buttons to set the label text to bold and italic.
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!Elbowed line
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* Click the '''Save & Close''' button to save and exit Quick Edit.
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|[[Image:Elbow.png]]
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<p>To create a line which is a composite of two or more lines, add an anchor point to one of the lines by using the right-click menu. Connect the end point of the other line to the anchor point as described above. Anchor points on lines can be moved by clicking and dragging to a desired position on the line.</p>
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{|class="prettytable"
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|-
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!Anchored line
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|-
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|[[Image:Anchor.png]]
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|}
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==== Right-click menu ====
 
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Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu. Some menu options are universal, and some depend ong the type of object you click.
 
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* Delete: Deletes the selected object
 
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* Select all: Selects all objects in the pathway
 
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* Select all DataNode objects: Selects all DataNode objects in the pathway, that is any object annotated as gene, protein, gene product, complex or RNA.
 
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* Add anchor: Adds an anchor point to a line, for connecting to other objects.
 
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* Anchor type>Circle: Displays the line anchor as a circle. This menu option is only available for a line anchor object.
 
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* Anchor type>None: Displays the line anchor as a small square. This menu option is only available for a line anchor object.
 
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* Line type>Curved: Creates a curved line, which can be customized in shape by connecting the end points to objects and by dragging the way points on the line. Way points appear as blue diamond shapes on the curved line.
 
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* Line type>Elbow: Creates an elbow line, which can be customized in shape by connecting the end points to objects and by dragging the way points on the line. Way points appear as blue diamond shapes on the curved line.
 
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* Line type>Straight: Creates a straight line.
 
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* Order>Bring to front: Brings the selected object to the front
 
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* Order>Send to back: Sends the selected object to the back
 
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* Order>Bring forward: Brings the selected object forward one layer
 
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* Order>Send backward: Sends the selected object backward one layer
 
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* Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.
 
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* Properties: '''Comments''', '''Literature''' and '''Annotation''' for objects can be viewed and edited through the Properties window.
 
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==== Save to WikiPathways.org ====
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= Editing Pathway Page text fields =  
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You can save your pathway directly to WikiPathways by clicking the "Save the pathway to WikiPathways.org" [[Image:SavetoWP.png]] button in the toolbar.
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Text fields on '''Pathway Page''' is edited like any other text on a wiki. Please refer to the [http://meta.wikimedia.org/wiki/Help:Wikitext WikiMedia] website for details on formatting.
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== Editing text fields ==  
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=== Description ===
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Text fields on ''Pathway Page'' is edited like any other text on a wiki. Please refer to the [http://meta.wikimedia.org/wiki/Help:Wikitext WikiMedia] website for details on formatting.
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Each '''Pathway Page''' includes a '''Description''' section, which contains information about the biological process described in the pathway. The '''Description''' can be edited by clicking the Edit link to the right of the Description section.
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==== Description ====
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=== Quality Tags ===
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Each ''Pathway Page'' includes a '''Description''' section, which contains information about the biological process described in the pathway. The ''Description'' can be edited by clicking the Edit link to the right of the Description section.
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'''Quality tags''' can be added to a pathway to notify the author and community about the state of the pathway. For example, you could tag a pathway that isn't annotated properly or tag your own pathway as work in progress. Quality Tags can be added by clicking the green plus sign icon in the Quality Tags section. Choose the type of Quality Tag from the drop-down list and enter a comment if appropriate.
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==== Bibliography ====
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=== Bibliography ===
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Each ''Pathway Page'' includes a '''Bibliography''' section, designed to hold reference information relevant to the pathway. When editing a pathway in the editor, any references to publications, textbooks and websites can be added to this section by right-clicking on any object in the pathway and selecting ''Add'' or ''Edit'' from the ''Literature'' menu. Details on how to incorporate literature references can be found [[:Help:LiteratureReferences|here]].
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Each '''Pathway Page''' includes a '''Bibliography''' section, designed to hold reference information relevant to the pathway. When editing a pathway in the editor, any references to publications, textbooks and websites can be added to this section by right-clicking on any object in the pathway and selecting '''Add''' or '''Edit''' from the '''Literature''' menu. Details on how to incorporate literature references can be found [[:Help:LiteratureReferences|here]].
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==== Curation Tags ====
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=== Ontology Tags ===
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The ''Ontology Tags'' section contains any ontology tags added to the pathway, and an interface for adding ontology tags. To add ontology tags, click the ''Add Ontology tags!'' link, which will open two tools for finding and adding ontology tags: a search interface and browsable trees for the supported ontologies. To search for a term, simply begin typing in the ''Search'' field. Pick a term from the results and click the ''Add'' button (green check mark) to add the term. Alternatively, find a term from the browsable ontology trees, select it and click the ''Add'' button. You can delete any ontology term from the pathway by selecting it and clicking the ''Remove'' button (red x). To learn more about a particular term, click the ''View more info on BioPortal!'' button (blue i).
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The '''Ontology Tags''' section contains any ontology tags added to the pathway and an interface for adding ontology tags. To add ontology tags, click the '''Add Ontology tags''' link, which will open two tools for finding and adding ontology tags: a search interface and browsable trees for the supported ontologies. To search for a term, simply begin typing in the ''Search'' field. Pick a term from the results and click the ''Add'' button (green check mark) to add the term. Alternatively, find a term from the browsable ontology trees, select it and click the '''Add''' button. You can delete any ontology term from the pathway by selecting it and clicking the '''Remove''' button (red x). To learn more about a particular term, click the '''View more info on BioPortal''' button (blue i).
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==== Categories ====
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= Editing Guidelines =
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Categories
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Each pathway is categorized into one or several categories, listed under ''Categories''. The category assignment can be edited or new categories added to the pathway by clicking the Edit link to the right of the Categories section.
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==== Creating a new pathway ====
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=== Best practices ===
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You can create a new pathway at WikiPathways by clicking the [[:Special:CreatePathwayPage|Create new pathway]] link in the navigation panel on the left side of each page. For details on how to create a new pathway, refer to the [[:Help:New Contributor Quickstart|New Contributor Quickstart]] guide.
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* Our comprehensive [http://wikipathways.org/img_auth.php/d/d0/Instructions_for_WikiPathways_Authors.pdf Instructions for Authors] outlines how to author pathways from a beginner's perspective and includes recommendations for best practices for authoring pathways.
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* The [[:Help:Guidelines_EditorPalette|Editor Palette guide]] describes the recommended utilization of the most commonly used elements of the WikiPathways editor palette. Examples are taken directly from the WikiPathways archives.
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=== General Guidelines ===
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* Complete pathway authoring guidelines are available [[:Help:Guidelines|here]].
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= Creating a new pathway =
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To create a pathway, you can either:
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* Use the PathVisio webstart editor at WikiPathways. <span style="color:#ff0000">'''Note: This option is currently unavailable.''' </span>
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* Upload an existing gpml via the '''Upload File''' option.
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* Create a pathway in PathVisio and upload it to WikiPathways via the [[:Help:WPClientPluginCuration|WikiPathways plugin for PathVisio]].  
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For details on how to create a new pathway, refer to the [[:Help:New_Contributor_Quickstart#Create_a_new_pathway_at_WikiPathways|'''New Contributor Quickstart''']] guide.
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Deleting_Pathways|Continue to Deleting pathways]]</p>
<p>[[:Help:Deleting_Pathways|Continue to Deleting pathways]]</p>

Current revision


The main editor for WikiPathways is a webstart version of PathVisio. You can also edit data node annotation and style directly at WikiPathways using the Quick Edit feature.

Editing in PathVisio Webstart

Each pathway page at WikiPathways has an Launch Editor button, which launches PathVisio webstart with the pathway in question loaded. This utilizes the WikiPathways Client plugin.

  • Click the Launch Editor button on any Pathway Page to open the PathVisio program with the current pathway loaded. You can add, edit or delete content from the pathway and when you save, updated versions of the images, controlled text, and data files are generated and are immediately available. For instructions on basic editing features please refer to PathVisio documentation.
  • Save your pathway by clicking Plugins > WikiPathways > Update. You will be asked to describe your edits.

Editing using Quick Edit

We have a new, quick way to edit data node annotations and styles. When logged in, the Quick Edit button is located at the bottom center of the pathway view. Clicking the Quick Edit button opens the editor:

Image:QuickEdit.png

Editing data node annotation

  • Open Quick Edit.
  • Select any data node to display its current annotation in the annotation tab.
  • To search for a new identifier, type in a gene name or label in the Search by name field and click the green Search button. Results are displayed in a separate results panel. Select an identifier from the list of results to assign it to the node.
  • To change only the data node type or data source, simply select from the drop-down lists.
  • To manually change the label or identifier, simply type directly in the corresponding field.
  • Click the Save & Close button to save and exit Quick Edit.

Editing data node style

  • Open Quick Edit.
  • Select a data node and click the Properties tab in Quick Edit.
  • Use the color chooser to change the border and label color of the node, or use the buttons to set the label text to bold and italic.
  • Click the Save & Close button to save and exit Quick Edit.


Editing Pathway Page text fields

Text fields on Pathway Page is edited like any other text on a wiki. Please refer to the WikiMedia website for details on formatting.

Description

Each Pathway Page includes a Description section, which contains information about the biological process described in the pathway. The Description can be edited by clicking the Edit link to the right of the Description section.

Quality Tags

Quality tags can be added to a pathway to notify the author and community about the state of the pathway. For example, you could tag a pathway that isn't annotated properly or tag your own pathway as work in progress. Quality Tags can be added by clicking the green plus sign icon in the Quality Tags section. Choose the type of Quality Tag from the drop-down list and enter a comment if appropriate.

Bibliography

Each Pathway Page includes a Bibliography section, designed to hold reference information relevant to the pathway. When editing a pathway in the editor, any references to publications, textbooks and websites can be added to this section by right-clicking on any object in the pathway and selecting Add or Edit from the Literature menu. Details on how to incorporate literature references can be found here.

Ontology Tags

The Ontology Tags section contains any ontology tags added to the pathway and an interface for adding ontology tags. To add ontology tags, click the Add Ontology tags link, which will open two tools for finding and adding ontology tags: a search interface and browsable trees for the supported ontologies. To search for a term, simply begin typing in the Search field. Pick a term from the results and click the Add button (green check mark) to add the term. Alternatively, find a term from the browsable ontology trees, select it and click the Add button. You can delete any ontology term from the pathway by selecting it and clicking the Remove button (red x). To learn more about a particular term, click the View more info on BioPortal button (blue i).

Editing Guidelines

Best practices

  • Our comprehensive Instructions for Authors outlines how to author pathways from a beginner's perspective and includes recommendations for best practices for authoring pathways.
  • The Editor Palette guide describes the recommended utilization of the most commonly used elements of the WikiPathways editor palette. Examples are taken directly from the WikiPathways archives.

General Guidelines

  • Complete pathway authoring guidelines are available here.

Creating a new pathway

To create a pathway, you can either:

  • Use the PathVisio webstart editor at WikiPathways. Note: This option is currently unavailable.
  • Upload an existing gpml via the Upload File option.
  • Create a pathway in PathVisio and upload it to WikiPathways via the WikiPathways plugin for PathVisio.

For details on how to create a new pathway, refer to the New Contributor Quickstart guide.

Return to Help Contents

Continue to Deleting pathways

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