Help:Editing Pathways
From WikiPathways
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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 webstart version of the 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. | ||
| + | Try it out in the [[:Pathway:Human:Sandbox|Sandbox pathway]]! | ||
| - | + | == Editing the pathway image == | |
| - | + | 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 [http://wiki.bigcat.unimaas.nl/pathvisio/Help PathVisio Help] and [http://wiki.bigcat.unimaas.nl/pathvisio/PathVisio_FAQ 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. | In addition to the drawing features described for the PathVisio webstart program, the WikiPathways embedded editor has some additional features. | ||
| - | + | == Save to WikiPathways.org == | |
You can save your pathway directly to WikiPathways by clicking the green check mark button in the toolbar. A button is also available for discarding the pathway (red stop sign). | You can save your pathway directly to WikiPathways by clicking the green check mark button in the toolbar. A button is also available for discarding the pathway (red stop sign). | ||
| - | + | == Right-click menu == | |
Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu: | Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu: | ||
* Delete: Deletes the selected object | * Delete: Deletes the selected object | ||
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* Edit literature reference: Any existing literature references can be edited | * Edit literature reference: Any existing literature references can be edited | ||
* Properties: '''Comments''', '''Literature''' and '''Annotation''' for objects can be viewed and edited through the Properties window. '''Comments''' and '''Literature''' can also be added and modified at the pathway-level, by accessing the Properties window from any blank space on the drawing board. | * Properties: '''Comments''', '''Literature''' and '''Annotation''' for objects can be viewed and edited through the Properties window. '''Comments''' and '''Literature''' can also be added and modified at the pathway-level, by accessing the Properties window from any blank space on the drawing board. | ||
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| - | + | == Editing text fields == | |
| - | + | 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. | |
| - | + | == 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. | |
| - | + | == 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 anywhere on the drawing board 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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| - | + | == Categories == | |
| - | + | Categories | |
| + | 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. | ||
| - | + | == Creating a new pathway == | |
| - | + | 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. | |
| - | + | == Deleting a pathway == | |
| - | + | A ''Pathway Page'' can only be deleted by an administrator. If you want to delete a pathway you have created, contact the Help Desk. | |
| - | </ | + | <p>[[:Help:Contents|Return to Help Contents]]</p> |
| + | <p>[[:Help:Watching_Pathways|Continue to Watching Pathways]]</p> | ||
Revision as of 23:14, 18 April 2008
In addition to editing the text fields on a given Pathway Page, this wiki also supports the ability to edit the pathway itself! Click on Edit pathway on any Pathway Page and a webstart version of the 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.
Try it out in the Sandbox pathway!
Editing the pathway image
Pathway editing for WikiPathways is done in an embedded version of the 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 PathVisio Help and PathVisio FAQ. In addition to the drawing features described for the PathVisio webstart program, the WikiPathways embedded editor has some additional features.
Save to WikiPathways.org
You can save your pathway directly to WikiPathways by clicking the green check mark button in the toolbar. A button is also available for discarding the pathway (red stop sign).
Right-click menu
Right-clicking anywhere on the drawing board or on an object will bring up the right-click menu:
- Delete: Deletes the selected object
- Select all: Selects all objects in the pathway
- Select all DataNode objects: Selects all gene objects in the pathway
- Order>Bring to front: Brings the selected object to the front
- Order>Send to back: Sends the selected object to the back
- Add literature reference: Literature references can be added for any object by entering a PMID or by manually entering information on authors, journal etc.
- Edit literature reference: Any existing literature references can be edited
- Properties: Comments, Literature and Annotation for objects can be viewed and edited through the Properties window. Comments and Literature can also be added and modified at the pathway-level, by accessing the Properties window from any blank space on the drawing board.
Editing 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.
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 anywhere on the drawing board and selecting Add or Edit from the Literature menu. Details on how to incorporate literature references can be found here.
Categories
Categories 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.
Creating a new pathway
You can create a new pathway at WikiPathways by clicking the 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 New Contributor Quickstart guide.
Deleting a pathway
A Pathway Page can only be deleted by an administrator. If you want to delete a pathway you have created, contact the Help Desk.
