Current revision

Welcome to WikiPathways! This guide presents a quick overview of the most common use cases of WikiPathways.

Where do you want to start?

Browse pathway archives or find a specific pathway

To get an overview of the WikiPathways archives, select the Browse thumbnail on the main page. You can browse pathways by species, and fine-tune the results by Collection. Results can be viewed as thumbnail images or a list.
To find a specific pathway, search for it by name, data node name, data node identifier or keyword.

For details Search and Browse, see Finding Pathways.

Edit an existing pathway

Become part of the WikiPathways community by creating a user account.
Find a pathway to edit.
To identify a pathway that is in need of editing, use the quality tag system. You can find lists of pathways organized by curation tag. For example, pathways tagged with the "Annotate nodes" tag or the "Fix interactions" tag can be greatly improved by relatively simple editing. You can also find a pathway through search or browse.

Pathway Diagram

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.

If you directly want to start editing, please download the local PathVisio installation from the PathVisio website, and install the WikiPathways plugin from within PathVisio.

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.

The content at WikiPathways is diverse in both style and content. While we don't enforce a particular drawing style, there are some guidelines for editing and graphical style. Our guidelines include general editing guidelines, a guide to the editor's palette, as well as a list of example pathways for your reference. There is also a specific process for including pathways into specific pathway collections at WikiPathways, read more about it here.

Additional fields of the pathway page

In addition to the graphical pathway representation, the Pathway Page has additional information fields that can be edited.

Add or remove relevant quality tags. For example, if you added database references to all unassigned DataNodes on the pathway, remove the "Annotate nodes" tag by clicking the Remove button next to the tag. Similarly, to add a quality tag, click the New tag button at the bottom of the Quality Tags section and select a tag from the drop-down menu. For example, if you consider the pathway incomplete, add the "Needs work" tag.
To edit the pathway description, click the Edit link in the Description section.
Add relevant ontology tags by searching for tags or by browsing the three ontologies.

Create a new pathway at WikiPathways

Become part of the WikiPathways community by creating a user account.
To create a pathway, you can either upload an existing gpml via the Upload File option, or create a pathway in PathVisio and upload it to WikiPathways via the WikiPathways plugin for PathVisio.

Upload gpml

You can also upload an existing gpml via the Upload File option on the Create new pathway page. Make sure the existing gpml contains a species designation.

PathVisio

You can upload a local gpml directly from PathVisio by opening the pathway in PathVisio, and then selecting Plugins > WikiPathways > Upload New. Make sure the pathway contains a species designation.

Guide for New Authors

Be sure to consult the Guide for New Authors for pathway modeling tips.

@@ Line 1: / Line 1: @@
 __NOTOC__
 <font size=2>
-''' Welcome to WikiPathways!''' </font> This guide let's you quickly get started with authoring pathways at WikiPathways, with step-by-step examples of the most common use cases.
+''' Welcome to WikiPathways!''' </font> This guide presents a quick overview of the most common use cases of WikiPathways.
-<br />'''''Where do you want to start?'''''<br />
+'''''Where do you want to start?'''''
-== Edit an existing pathway ==
+= Browse pathway archives or find a specific pathway =
+# To get an overview of the WikiPathways archives, select the '''Browse''' thumbnail on the main page. You can browse pathways by species, and fine-tune the results by '''Collection'''. Results can be viewed as thumbnail images or a list.
+# To find a specific pathway, search for it by name, data node name, data node identifier or keyword.
+For details '''Search''' and '''Browse''', see [[:Help:Finding_Pathways|Finding Pathways]].
+= Edit an existing pathway =
 # Become part of the WikiPathways community by [[:Special:Userlogin|creating a user account]].
-# Find a pathway to edit. <br />To identify a pathway that is in need of editing, use the [[:Help:CurationTags|curation tag system]]. You can find [[:Special:SpecialCurationTags|lists of pathways]] organized by curation tag. For example, pathways tagged with the "Missing gene/protein database references" (MissingXRef) tag or the "Unconnected lines" (NoInteractions) tag can be greatly improved by relatively simple editing. You can also find a pathway through [[:Help:Finding Pathways|search or browse]].<br />
+# Find a pathway to edit. <br />To identify a pathway that is in need of editing, use the [[:Help:QualityTags|quality tag system]]. You can find [[:Special:SpecialCurationTags|lists of pathways]] organized by curation tag. For example, pathways tagged with the "Annotate nodes" tag or the "Fix interactions" tag can be greatly improved by relatively simple editing. You can also find a pathway through [[:Help:Finding Pathways|search or browse]].<br />
-==== Graphical pathway representation ====
+=== Pathway Diagram ===
-# Once you decide on a pathway to edit, open the [[:Help:Viewing Pathways|''Pathway Page'']] for that pathway.
+'''The editor for WikiPathways is the local version of PathVisio.'''
-# Click the ''Edit pathway'' link under the pathway image. This will open the pathway in an embedded version of the PathVisio program, where you can [[:Help:Editing Pathways|edit]] the pathway.
-:The content at WikiPathways is diverse in both style and content. While we don't enforce a particular drawing style, there are some guidelines for editing and graphical style. Our guidelines include [[:Help:Guidelines|general editing guidelines]] as well as a [[:Help:Guidelines#Example_pathways|list of example pathways]] for your reference. There is also a specific process for including pathways into specific pathway collections at WikiPathways, read more about it [[:Help:Guidelines#Inclusion_of_pathways_into_specific_pathway_collections|here]]. For detailed instructions on how to use the PathVisio editor, please refer to [http://www.pathvisio.org/wiki/PathVisioHelp PathVisio Help].
+* 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.
-:When you are done editing, save the pathway in PathVisio by clicking the "Close the editor" button and then return to the ''Pathway Page''. Click the ''Refresh'' button in your browser to view your recent changes.<br />
-==== Additional fields of the pathway page ====
+* 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.
+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].
+* Save your pathway by clicking '''Plugins > WikiPathways > Update'''. You will be asked to describe your edits.
+The content at WikiPathways is diverse in both style and content. While we don't enforce a particular drawing style, there are some guidelines for editing and graphical style. Our guidelines include [[:Help:Guidelines|general editing guidelines]], [[:Help:Guidelines_EditorPalette|a guide to the editor's palette]], as well as a [[:Help:Guidelines#Example_pathways|list of example pathways]] for your reference. There is also a specific process for including pathways into specific pathway collections at WikiPathways, read more about it [[:Help:Guidelines#Inclusion_of_pathways_into_specific_pathway_collections|here]].
+=== Additional fields of the pathway page ===
 In addition to the graphical pathway representation, the [[:Help:Viewing_Pathways|Pathway Page]] has additional information fields that can be edited.
-# Add or remove relevant curation tags. For example, if you added database references to all unassigned DataNodes on the pathway, remove the "Missing gene/protein database references" tag by clicking the ''Remove'' button next to the tag. Similarly, to add a curation tag, click the ''New tag'' button at the bottom of the Curation Tags section and select a tag from the drop-down menu. For example, if you consider the pathway incomplete, add the "Needs work" tag.
+# Add or remove relevant quality tags. For example, if you added database references to all unassigned DataNodes on the pathway, remove the "Annotate nodes" tag by clicking the '''Remove''' button next to the tag. Similarly, to add a quality tag, click the '''New tag''' button at the bottom of the Quality Tags section and select a tag from the drop-down menu. For example, if you consider the pathway incomplete, add the "Needs work" tag.
-# To edit the pathway description, click the Edit link in the Description section.
+# To edit the pathway description, click the '''Edit''' link in the '''Description''' section.
-# Add categories to the pathway by clicking the Edit button in the Categories section.
+# Add relevant ontology tags by searching for tags or by browsing the three ontologies.
-== Create a new pathway at WikiPathways ==
+= Create a new pathway at WikiPathways =
 # Become part of the WikiPathways community by [[:Special:Userlogin|creating a user account]].
-# Click the [[:Special:CreatePathwayPage|Create]] thumbnail on the main page or click the ''Create'' link in the left navigation panel.
+# To create a pathway, you can either '''upload an existing gpml via the '''Upload File''' option, or '''create a pathway in PathVisio and upload it to WikiPathways''' via the [[:Help:WPClientPluginCuration|WikiPathways plugin for PathVisio]].
-# On the ''Create new pathway'' page, enter a name for the pathway and then select which species the pathway is for from the drop-down menu. Selecting the "Make pathway private" option hides your pathway from the rest of the community for 30 days. See the section on [[:Help:Private Pathways|Private Pathways]] for details. Click the ''Create pathway'' button to continue.
+=== Upload gpml ===
-# PathVisio will open with a blank drawing board. Create your pathway in PathVisio.<br />For information on editing guidelines, please review our [[:Help:Guidelines|genereal editing guidelines]] and our [[:Help:Guidelines#Example_pathways|list of example pathways]]. For instructions on how to use PathVisio, please refer to [http://www.pathvisio.org/wiki/PathVisioHelp PathVisio Help].<br />
+# You can also upload an existing gpml via the '''Upload File''' option on the [[:Special:CreatePathwayPage|Create new pathway]] page. Make sure the existing gpml contains a species designation.
-# When your pathway is complete, click the "Close the editor" button to submit your pathway to WikiPathways. A new browser window will open with the ''Pathway Page'' for your newly created pathway at WikiPathways.
-# Add information about your pathway by [[:Help:Editing Pathways|editing]] the text fields in the ''Pathway Page''. '''Remember to assign a category to your pathway so that the pathway will appear on the [[Special:BrowsePathwaysPage|browse page]] listing all categorized pathways at WikiPathways.
-== Transfer pathway from GenMAPP to WikiPathways ==
+=== PathVisio ===
-You can transfer a pathway that you have created in the GenMAPP program to WikiPathways.
+You can upload a local gpml directly from PathVisio by opening the pathway in PathVisio, and then selecting '''Plugins > WikiPathways > Upload New'''. Make sure the pathway contains a species designation.
-# Become part of the WikiPathways community by [[:Special:Userlogin|creating a user account]].
-# Click the [[:Special:CreatePathwayPage|Create]] thumbnail on the main page or click the ''Create'' link in the left navigation panel.
-# On the ''Create new pathway'' page, enter a name for the pathway and then select which species the pathway is for from the drop-down menu. Click the ''Create pathway'' button to continue.
-# PathVisio will open with a blank drawing board. To access your existing GenMAPP pathway, go to ''File>Import'' and select the appropriate .mapp file.
-# Make any necessary changes to the pathway in the PathVisio.
-# When your pathway is complete, click the "Close the editor" button to submit your pathway to WikiPathways. A new browser window will open with the ''Pathway Page'' for your newly created pathway at WikiPathways.
-# Add information about your pathway by [[:Help:Editing Pathways|editing]] the text fields in the ''Pathway Page''. Remember to assign a category to your pathway so that the pathway will appear in the lists of all pathways at WikiPathways.
-<p>[[:Help:Contents|Return to Help Contents]]</p>
+=== Guide for New Authors ===
-<p>[[:Help:Finding_Pathways|Continue to Finding Pathways]]</p>
+* Be sure to consult the [http://wikipathways.org/img_auth.php/d/d0/Instructions_for_WikiPathways_Authors.pdf Guide for New Authors] for pathway modeling tips.

Help:New Contributor Quickstart

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Browse pathway archives or find a specific pathway

Edit an existing pathway

Pathway Diagram

Additional fields of the pathway page

Create a new pathway at WikiPathways

Upload gpml

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Guide for New Authors

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