WikiPathways: Difference between revisions

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Link/URL:	http://www.wikipathways.org
What:	WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
Who:	WikiPathways is maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (University of California, San Francisco). The current WikiPathways team includes Thomas A.J. Kelder, Alexander R. Pico, Martijn van Iersel, Kristina Hanspers, Bruce R. Conklin and Chris T.A. Evelo.
Updates:	Currently in Beta; new releases every 3 weeks.
Upcoming events:
Web Services:	Coming soon... Currently have batch download options avaiable here.
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About WikiPathways

WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

Content

Biological pathways from multiple species representing metabolism, signaling, gene regulation, physiological functions and more...

Using WikiPathways

Each pathway at WikiPathways has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists. Any pathway can be edited from within its wiki page by activating an embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate particular pathways by name, by the genes and proteins they contain, or by the text displayed in their descriptions and comments. One can also browse the collection of pathways with combinations of species names and ontology-based categories. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML, which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.

Browsing

Browse the WikiPathways archive by species and category.

Searching

Search the WikiPathways archive by pathway name, gene/protein name, or description keyword.

Usage examples

We are promoting various pathway curation and user communities through the use of Portals through MediaWiki. Here are a few early examples:

Plants - under construction
GenMAPP - under construction
BiGCaT - under construction

Technology

MediaWiki - for basic wiki functionality
PathVisio - for embedded pathway drawing and editing

Discussion

References

Manuscript in preparation

External Links

WikiPathways URL:http://www.wikipathways.org

Discussion of WikiPathways on other websites

GenMAPP at WikiPathways - link
Pathguide listing of WikiPathways.

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 [[Category:Databases]]
+[[Category:Biology wikis]]
+[[Category:Pathway Databases]]
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-!{{table heading style}} |Link/URL:
+!align=left {{table heading style}} |Link/URL:
+||
+http://www.wikipathways.org
 |-
-!{{table heading style}} |What:
+!align=left {{table heading style}} |What:
+||
+WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
 |-
-!{{table heading style}} |Who:
+!align=left {{table heading style}} |Who:
+||
+WikiPathways is maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (University of California, San Francisco). The current WikiPathways team includes Thomas A.J. Kelder, Alexander R. Pico, Martijn van Iersel, Kristina Hanspers, Bruce R. Conklin and Chris T.A. Evelo.
 |-
-!{{table heading style}} |Updates:
+!align=left {{table heading style}} |Updates:
+||
+Currently in Beta; new releases every 3 weeks.
 |-
-!{{table heading style}} |Upcoming events:
+!align=left {{table heading style}} |Upcoming events:
+||
 |-
-!{{table heading style}} |Web Services:
+!align=left {{table heading style}} |Web Services:
-|-
+||
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+Coming soon...
+Currently have batch download options avaiable [http://wikipathways.org/index.php/Download_Pathways here].
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 {{Database_table_help}}
 ==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
-''Add general information here''
+[{{{1|http://www.wikipathways.org}}} {{PAGENAME}}] was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as [http://www.genome.jp/kegg/ KEGG], [http://www.reactome.org/ Reactome] and [http://www.pathwaycommons.org/pc/ Pathway Commons]. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
-[{{{1|link}}} {{PAGENAME}}] is...
 ==Content {{HelpIcon|Help:Databases}}==
+Biological pathways from multiple species representing metabolism, signaling, gene regulation, physiological functions and more...
 ==Using {{PAGENAME}} {{HelpIcon|Help:Databases}}==
+Each pathway at WikiPathways has a dedicated wiki page, displaying the current diagram, description, references, download options, version history, and component gene and protein lists. Any pathway can be edited from within its wiki page by activating an embedded pathway editor. After editing, an updated pathway image is displayed on the wiki page along with the version history and list of component genes and proteins. Users can easily monitor and undo changes, compare differences and search for overlapping pathways. Using the search feature, one can locate particular pathways by name, by the genes and proteins they contain, or by the text displayed in their descriptions and comments. One can also browse the collection of pathways with combinations of species names and ontology-based categories. The pathway content at WikiPathways is freely available for download in a variety of data and image formats, including GPML, which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape, GenMAPP and PathVisio.
 ===Browsing===
+[http://wikipathways.org/index.php/Special:BrowsePathwaysPage Browse] the WikiPathways archive by species and category.
 ===Searching===
+Search the WikiPathways archive by pathway name, gene/protein name, or description keyword.
 ===Usage examples===
-''Add links to additional pages describing success stories here.''
+We are promoting various pathway curation and user communities through the use of Portals through MediaWiki. Here are a few early examples:
+* [http://wikipathways.org/index.php/Portal:Plants Plants] - ''under construction''
+* [http://wikipathways.org/index.php/Portal:GenMAPP GenMAPP] - ''under construction''
+* [http://wikipathways.org/index.php/Portal:BiGCaT BiGCaT] - ''under construction''
 ==Other sites with related content {{HelpIcon|Help:Databases}}==
+* [http://www.genome.jp/kegg/ KEGG]
+* [http://www.reactome.org/ Reactome]
+* [http://www.pathwaycommons.org/pc/ Pathway Commons]
 ==Technology {{HelpIcon|Help:Databases}}==
-===Web Services/API===
+* [http://www.mediawiki.org/wiki/MediaWiki MediaWiki] - for basic wiki functionality
+* [http://www.pathvisio.org/Main_Page PathVisio] - for embedded pathway drawing and editing
 ==Discussion {{HelpIcon|Help:Databases}}==
 ==References {{HelpIcon|Help:Databases}}==
-<references />
+* Manuscript in preparation
 ==External Links==
-[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
+[{{{1|http://www.wikipathways.org}}} {{PAGENAME}}] URL:{{{1|http://www.wikipathways.org}}}
 ===Discussion of {{PAGENAME}} on other websites===
+* GenMAPP at WikiPathways - [http://www.genmapp.org/showcase.html link]
+* [http://www.pathguide.org/ Pathguide] listing of WikiPathways.