Help:Editing Pathways

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'''The main editor for WikiPathways is PathVisio. You can also edit  data node annotation and style directly at WikiPathways using the QuickEdit feature.'''
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= Editing Pathway content through PathVisio: =
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'''The editor for WikiPathways is the local version of PathVisio.'''
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{{#ev:youtube|tYD9JxILxv8|700|left|Intro to Editing Video}}
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* If you have never edited or built a pathway model before, we would advise you to use our online learning tool [http://academy.wikipathways.org/ WikiPathways Academy] first.
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* If you directly want to start editing, please download the [https://www.pathvisio.org/downloads local PathVisio installation] from the PathVisio website, and install the [https://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways plugin] from within PathVisio.
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Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done [http://plugins.pathvisio.org/wp-client/request-webservice-access/ here] or through sending a message to our team on our [https://groups.google.com/forum/#!forum/wikipathways-discuss google discussion forum].
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* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.
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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]].
__NOTOC__
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= Editing in PathVisio =
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<!--
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{{#ev:youtube|tYD9JxILxv8|700|left|Intro to Editing Video}}
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Each pathway page at WikiPathways has an '''Edit pathway''' button, which launches [http://www.pathvisio.org PathVisio] with the pathway in question loaded. This utilizes the [[:Help:WPClientPluginCuration|WikiPathways Client plugin]].
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= Editing in PathVisio Webstart =
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* Click on the '''Edit pathway''' 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.
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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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PathVisio supports a number of common drawing tools, as well as an interface for linking objects on pathways to an underlying gene database. For instructions on basic editing features please refer to [http://www.pathvisio.org/documentation/editing-and-viewing-pathways/ PathVisio documentation].  
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* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.  
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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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-->
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= Editing using QuickEdit =
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<!--
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We have a new, quick way to edit data node annotations and styles. When logged in, the QuickEdit button is located at the bottom center of the pathway view. Clicking the QuickEdit button opens the editor:
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= Editing using Quick Edit =
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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:
[[Image:QuickEdit.png]]
[[Image:QuickEdit.png]]
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=== Editing data node annotation ===
=== Editing data node annotation ===
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* Open QuickEdit.
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* Open Quick Edit.
* Select any data node to display its current annotation in the annotation tab.
* 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 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 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.
* To manually change the label or identifier, simply type directly in the corresponding field.
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* Click the '''Save & Close''' button to save and exit QuickEdit.
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* Click the '''Save & Close''' button to save and exit Quick Edit.
=== Editing data node style ===
=== Editing data node style ===
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* Open QuickEdit.
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* Open Quick Edit.
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* Select a data node and click the '''Properties''' tab in QuickEdit.
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* 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.
* 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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* Click the '''Save & Close''' button to save and exit QuickEdit.
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* Click the '''Save & Close''' button to save and exit Quick Edit.
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-->
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= Editing Pathway Page directly on the website: =
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Text fields on a '''Pathway Page''' can be 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 Pathway Page 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.
=== Quality Tags ===
=== 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.
'''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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=== Description ===
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=== Ontology 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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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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<!-- Not possible to edit on website.
=== Bibliography ===
=== 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 [[:Help:LiteratureReferences|here]].
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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=== Ontology Tags ===
 
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The '''Ontology Tags''' section contains any ontology tags added to the pathway. The interface for adding and editing ontology tags is currently disabled. A new version will be available in the future.
 
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<!--
 
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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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=== Creating a new pathway ===
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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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= Editing Guidelines =
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=== Best practices ===
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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.
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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


Editing Pathway content through PathVisio:

The editor for WikiPathways is the local version of PathVisio.

  • If you have never edited or built a pathway model before, we would advise you to use our online learning tool WikiPathways Academy first.

Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done here or through sending a message to our team on our google discussion forum.

  • Save your pathway by clicking Plugins > WikiPathways > Update. You will be asked to describe your edits.


Editing Pathway Page directly on the website:

Text fields on a Pathway Page can be 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.

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.
  • 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

Retrieved from "https://classic.wikipathways.org/index.php/Help:Editing_Pathways"
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