Help:Editing Pathways

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__NOEDITSECTION__ <!-- Turn off section editing -->
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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! There are three options for editing a pathway at WIkiPathways:
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= Editing Pathway content through PathVisio: =
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* Edit any pathway in [http://www.pathvisio.org PathVisio], using the [http://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways plugin]
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'''The editor for WikiPathways is the local version of PathVisio.'''
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* '''COMING SOON:''' Make edits to data node annotation and style using the QuickEdit feature.
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* Edit the pathway directly at WikiPathways using the embedded version of PathVisio.
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= Editing in PathVisio with WikiPathways plugin =
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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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{{Help:WPClientPluginCuration}}
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= Editing using QuickEdit =
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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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'''COMING SOON'''
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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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We are developing a new javascript pathway editor and the first version is a QuickEdit feature for editing data node annotation and style. 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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* 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]].
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__NOTOC__
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<!--
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{{#ev:youtube|tYD9JxILxv8|700|left|Intro to Editing Video}}
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= Editing in PathVisio Webstart =
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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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* 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 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.
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* Select any data node to display its annotation in the annotation fields.
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* 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.
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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 or italic.
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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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* 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 in the embedded PathVisio editor =
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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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Clicking on '''Edit pathway''' on any '''Pathway Page''' opens an embedded version of 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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=== Description ===
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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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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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=== Quality Tags ===
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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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'''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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Below are brief instructions on the most commonly used editing features in PathVisio and the embedded PathVisio editor at WikiPathways.
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=== Ontology Tags ===
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<!--
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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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==== Adding, selecting, sizing and moving objects ====
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For instructions on basic editing features please refer =o [http://www.pathvisio.org/documentation/editing-and-viewing-pathways/ PathVisio documentation].
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-->
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==== Grouping objects ====
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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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<!-- Not possible to edit on website.
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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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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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==== Selecting grouped objects and complexes ====
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=== Bibliography ===
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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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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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{|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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-->
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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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{|class="prettytable"
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|-
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!Adding connectors
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|-
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|[[Image:Connectors.png]]
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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, segmented and composite lines ====
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= Editing Guidelines =
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For layout reasons and to properly represent biological interactions, non-straight lines are sometimes ideal. To create a curved, elbowed or segmented 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, Elbow or Segmented. The Curved option will produce a curved line with smooth edges, whereas the Elbow option will create a curved line with 90 degree edges. The Segmented option will let you define a line with one or more waypoints. 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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{|class="prettytable"
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|-
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!Elbowed line
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|-
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|[[Image:Elbow.png|300px]]
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|}
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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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<!--
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=== Best practices ===
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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 on 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 data node objects: Selects all data node 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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-->
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==== Save to WikiPathways.org ====
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Save your pathway by clicking the '''Save the pathway to WikiPathways.org''' button in the toolbar.
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= Editing Pathway Page text fields =
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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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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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==== Curation Tags ====
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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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'''Curation 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. Curation Tags can be added by clicking the green plus sign icon in the Curation Tags section. Choose the type of Curation Tag from the drop-down list and enter a comment if appropriate.
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==== Description ====
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=== General Guidelines ===
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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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==== Bibliography ====
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* Complete pathway authoring guidelines are available [[:Help:Guidelines|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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==== Ontology Tags ====
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= Creating a new pathway =
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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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To create a pathway, you can either:
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<!--
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* Use the PathVisio webstart editor at WikiPathways.  
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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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* Upload an existing gpml via the '''Upload File''' option.
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-->
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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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==== 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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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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