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 5: / Line 5: @@
 '''''Where do you want to start?'''''
-== Browse pathway archives or find a specific 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 or identifier or keyword.
+# 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 ==
+= 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, you have two options for editing the pathway:
+'''The editor for WikiPathways is the local version of PathVisio.'''
-## Open the [[:Help:Viewing Pathways|Pathway Page]] for the pathway and click the '''Edit pathway''' link under the pathway image. This will open the pathway in the WikiPathways editor, where you can [[:Help:Editing Pathways|edit]] the pathway.
-## Use the [[:Help:WPClientPluginCuration|WikiPathways plugin for PathVisio]] to 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]].
-: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 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.
+* 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.
 # 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]].
-# To create a pathway, you can either use the editor at WikiPathways (see below), or create a pathway in PathVisio and upload it to WikiPathways via the [[:Help:WPClientPluginCuration|WikiPathways plugin for PathVisio]].
+# 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]].
-# To create a pathway in the WikiPathways editor, click the [[:Special:CreatePathwayPage|Create]] thumbnail on the main page or click the '''Create''' link in the left navigation panel.
+=== Upload gpml ===
-# 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.
+# 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.
-# The WikiPathways editor contains a full set of drawing tools for pathway creation. See [[:Help:Editing_Pathways|Editing Pathways]] for details.
-For information on editing guidelines, please review our [[:Help:Guidelines|general editing guidelines]] and our [[:Help:Guidelines#Example_pathways|list of example pathways]].
-# When your pathway is complete, click the '''Close the editor''' button to save your pathway to WikiPathways. The '''Pathway Page''' for your newly created pathway will be displayed.
-# 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 using PathVisio. If you have the [http://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways] plugin installed in PathVisio, you can upload the pathway directly from PathVisio. Otherwise, you can save the pathway in gpml format and upload the pathway it to WikiPathways under '''Create new pathway'''.
+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]].
-# Launch PathVisio. 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 PathVisio.
-## If you have the WikiPathways plugin installed in PathVisio, select '''Plugins -> WikiPathways -> Upload New'''. You will be asked to specify your login information and a description of the pathway.
-## To upload the pathway without the plugin, 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 '''Upload file''' button to continue.
-## Select the gpml file using the file browser. There is also an option to make the pathway private, meaning it will be hidden from public view for 30 days. Click '''Upload pathway''' when done.
-# 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

From WikiPathways

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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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