WikiPathways

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<h2 class="frontPagePanel blueFg">Welcome to WikiPathways <sup>BETA</sup></h2>
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<h2 class="frontPagePanel redFg">Welcome to WikiPathways <sup>BETA</sup></h2>
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<font size=2>'''In the “tradition” of <span class=plainlinks>[http://wikipedia.org Wikipedia]</span> and other wiki platforms, WikiPathways is intended to be an open, public space for content editing dedicated to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community. [[WikiPathways:About|More about WikiPathways...]]'''</font></div>
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<font size=2>'''In the new tradition of <span class=plainlinks>[http://wikipedia.org Wikipedia]</span>, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. [[WikiPathways:About|More about WikiPathways...]]'''</font></div>
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<h2 class="frontPagePanel yellowFg">How To Find a Pathway</h2>
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<h2 class="frontPagePanel blueFg">Finding Pathways</h2>
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:There are many ways to find your pathways of interest. You can search by:
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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:* Name of the pathway
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|-
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:* Browse by species
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:* Browse by pathway categories
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|align="center" valign="top"|<big>'''Search'''</big>{{#googleCoop:}}
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:* Search by gene name (google search)
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|rowspan="2" align="center" valign="top"|<big>'''Browse'''</big>{{#imgLink:Browse_thumb_200.jpg|200|center||special||BrowsePathwaysPage|Browse}}
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'''Browse by species and category'''
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|-
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|align="left" valign="top"|'''You can search by:'''
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*Pathway name ''(Apoptosis)''
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*Gene or protein name ''(p53)''
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*Any page content ''(cancer)''
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<h2 class="frontPagePanel yellowFg">Viewing Pathways</h2>
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<h2 class="frontPagePanel blueFg">Contributing New Pathways</h2>
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:<big>'''Image'''</big>
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{|style="width:100%;" border="0" valign="top" cellspacing="2" cellpadding="1" align="center"
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:Once you are on a Pathway Page you can click on the image of the pathway to view the SVG representation.  The pathway image is available for download in SVG and PNG formats.
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:<big>'''Text'''</big>
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:Each Pathway Page has a text description, itemized gene list, references and relevant links.
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|align="center" valign="top"|<big>'''Create'''</big>{{#imgLink:Create_thumb_160.jpg|160|center||special||CreatePathwayPage|Create}}
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:<big>'''Data'''</big>
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'''Create a new pathway page'''
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:Each pathway is also available for download as a GPML data file (GenMAPP Pathway Markup Language), an XML for annotated, curated pathway content. This format can be used with [http://wiki.bigcat.unimaas.nl/pathvisio/Main_Page PathVisio].
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|rowspan="1" align="center" valign="top"|<big>'''Suggest'''</big>{{#imgLink:Wishlist_thumb_200.jpg|200|center||special||SpecialWishList|Wish list}}
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'''Add a pathway to the wish list'''
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<h2 class="frontPagePanel yellowFg">Editing Pathways</h2>
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<h2 class="frontPagePanel blueFg">Sample Pathway Pages</h2>
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:In addition to editing the text fields on a given Pathway Page, this wiki also support the ability to edit the pathway itself!  Click on "EDIT" and a webstart version of PathVisio will open with the current pathway loaded.  You can then add, edit or delete content from the pathway. When you save, updated version of the images, controlled text, and data files are generated and are immediately available.
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|-
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|rowspan="1" align="center" valign="top" style="width:45%;"|<big>'''Sandbox'''</big>{{#imgLink:Sandbox_thumb_200.jpg|200|center||pathway|Human|Sandbox|Sandbox}}
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'''Play with the editor tools'''
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'''Check out the following pages:'''<br>
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* [[Special:Recentchanges?namespace=102 | Show recent changes]]
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* [[Special:NewPathwaysPage | Show new pathways]]
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* [[Special:MostEditedPathwaysPage | Show most edited pathways]]
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* [[Special:PopularPathwaysPage | Show most viewed pathways]]
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'''For more information see the [[Help:Contents |Help pages]]'''
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|-
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:'''Try it out in the [[Pathway:Human:Sandbox | Sandbox]] pathway!'''
 
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:'''Also see the [[Help:Contents |Help pages]]'''
 
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<h2 class="frontPagePanel redFg">''UNDER CONSTRUCTION''</h2>
 
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'''This site is undergoing rigorous beta testing.  We are still implementing critical features and making major changes to these pages. Nevertheless, feel free to use the site to find, edit and create pathway content.'''
 
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If you have any questions or suggestions, you can post them to the [http://groups.google.com/group/wikipathways-user WikiPathways-Users Google Group], or email them directly to us: 
 
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Thomas Kelder: ''Thomas.Kelder[AT]BIGCAT.unimaas.nl''
 
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<br>
 
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Alex Pico: ''apico[AT]gladstone.ucsf.edu''
 
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Also see the [http://ftp2.bigcat.unimaas.nl/~martijn.vaniersel/mantis/my_view_page.php PathVisio bug tracker] for WikiPathways and PathVisio related bugs.
 
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<h2 class="frontPagePanel greenFg">New!</h2>
<h2 class="frontPagePanel greenFg">New!</h2>
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*Show other users which pathways you would like to see on WikiPathways, by adding them to the '''[[Special:SpecialWishlist|Pathway Wishlist]]'''.
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*Pathway [[Special:SpecialWishlist|Wish List]]
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*[[Special:BrowsePathwaysPage|Browse pathways]] in WikiPathways by cross-referencing species and categories!
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*New embedded pathway editor   
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*New pathway editor embedded into every [[{{PATHWAYOFTHEDAY}}|Pathway page]]. Edit pathways without opening an external editor!
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*[[Download Pathways|Batch download page]]  
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*[[Download Pathways|Batch download page]]: download all pathways as an archive of image or data files with a single click!
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*Visual diff tool for comparing pathway versions
<h2 class="frontPagePanel greenFg">Coming Soon...</h2>
<h2 class="frontPagePanel greenFg">Coming Soon...</h2>
* Additional Species:
* Additional Species:
** Fruit Fly
** Fruit Fly
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** Zebrafish
 
** C.elegans
** C.elegans
** Yeast
** Yeast
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* Visual comparison of different pathway versions
 
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<h2 class="frontPagePanel greenFg">Contents</h2>
 
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[[:Category:Human|Overview of all human pathways]]
 
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[[:Category:Mouse|Overview of all mouse pathways]]
 
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[[:Category:Rat|Overview of all rat pathways]]
 
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[[:Category:Cellular Process|Cellular Process category]]
 
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[[:Category:Metabolic Process|Metabolic Process category]]
 
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[[:Category:Physiological Process|Physiological Process category]]
 
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[[:Category:Molecular Function|Molecular Function category]]
 
<h2 class="frontPagePanel greenFg">Statistics</h2>
<h2 class="frontPagePanel greenFg">Statistics</h2>

Revision as of 14:38, 7 January 2008

<analytics uacct="UA-1605246-1" ></analytics>


Welcome to WikiPathways BETA

In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. More about WikiPathways...

Finding Pathways

Search{{#googleCoop:}} Browse
Title error

Browse by species and category

You can search by:
  • Pathway name (Apoptosis)
  • Gene or protein name (p53)
  • Any page content (cancer)

Contributing New Pathways

Create
Title error

Create a new pathway page

Suggest
Title error

Add a pathway to the wish list

Sample Pathway Pages

Sandbox
Sandbox

Play with the editor tools

Check out the following pages:

For more information see the Help pages


Today's featured pathway


Unable to get pathway of the day: FeaturedPathways doesn't contain any valid pathway!

New!

Coming Soon...

  • Additional Species:
    • Fruit Fly
    • C.elegans
    • Yeast

Statistics


  • There are 2792 pathways
  • Number of pathways (and unique genes) per species:
Anopheles gambiae: 20 (428)
Arabidopsis thaliana: 94 (956)
Bacillus subtilis: 3 (14)
Beta vulgaris: 1 (25)
Bos taurus: 274 (3743)
Caenorhabditis elegans: 66 (882)
Canis familiaris: 112 (2820)
Danio rerio: 105 (2708)
Drosophila melanogaster: 35 (565)
Escherichia coli: 12 (28)
Equus caballus: 12 (200)
Gallus gallus: 100 (2106)
Glycine max: 1 (2)
Gibberella zeae: 2 (0)
Homo sapiens: 1134 (8175)
Hordeum vulgare: 1 (9)
Mus musculus: 226 (4977)
Mycobacterium tuberculosis: 17 (148)
Oryza sativa: 69 (493)
Pan troglodytes: 116 (2937)
Populus trichocarpa: 5 (0)
Rattus norvegicus: 173 (3623)
Saccharomyces cerevisiae: 136 (856)
Solanum lycopersicum: 7 (5)
Sus scrofa: 9 (65)
Vitis vinifera: 1 (0)
Zea mays: 58 (31)
Plasmodium falciparum: 1 (0)
Brassica napus: 2 (162)
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