EcoliWiki - User contributions [en]

Letter to Science about wikifying genome information

2008-04-10T00:51:07Z

Apico: /* draft */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. David Lipman’s fears that "It would be chaos" are widely shared. These fears need to be balanced, however, by recognition that the expertise of individual curators is unlikely to encompass the collective, albeit intermittently applied, expertise of the larger scientific community (including the 250 signers of the Bidartondo et al. letter). Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki <ref>http://ecoliwiki.net</ref>, the community annotation component of the EcoliHub project <ref>http://ecolihub.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a wiki-based browser and annotation engine for Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/><ref>http://www.wikipathways.org</ref> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, but lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist and as part of the study of a specific scientific topic. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to ongoing discussion of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO terms at GONUTS.

===signatures===
* James C. Hu, Texas A&M University
* Rodolfo Aramayo, Texas A&M University
* Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
* Christine Elsik, Georgetown University
* Michael Gribskov, Purdue University
* Deborah A. Siegele, Texas A&M University
* Barry L. Wanner, Biological Sciences, Purdue University, West Lafayette, IN 47907
* Alexander R. Pico, The Gladstone Institutes, San Francisco
<references/>

----

Letter to Science about wikifying genome information

2008-04-10T00:50:07Z

Apico: /* draft */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. David Lipman’s fears that "It would be chaos" are widely shared. These fears need to be balanced, however, by recognition that the expertise of individual curators is unlikely to encompass the collective, albeit intermittently applied, expertise of the larger scientific community (including the 250 signers of the Bidartondo et al. letter). Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki <ref>http://ecoliwiki.net</ref>, the community annotation component of the EcoliHub project <ref>http://ecolihub.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a wiki-based browser and annotation engine for Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/><ref>http://www.wikipathways.org</ref> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, but lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist and as part of the study of a specific scientific topic. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to ongoing discussion of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

===signatures===
* James C. Hu, Texas A&M University
* Rodolfo Aramayo, Texas A&M University
* Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
* Christine Elsik, Georgetown University
* Michael Gribskov, Purdue University
* Deborah A. Siegele, Texas A&M University
* Barry L. Wanner, Biological Sciences, Purdue University, West Lafayette, IN 47907
* Alexander R. Pico, The Gladstone Institutes, San Francisco
<references/>

----

WikiPathways

2008-04-10T00:42:09Z

Apico: edited by Apico via TableEdit

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|
http://www.wikipathways.org
|-
!{{table heading style}} |What:
|
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
|-
!{{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:
|
Currently in Beta; new releases every 3 weeks.
|-
!{{table heading style}} |Upcoming events:
|
Manuscript in preparation. Biology Wiki Meeting in the Fall?
|-
!{{table heading style}} |Web Services:
|
Coming soon...
Currently have batch download options avaiable [http://wikipathways.org/index.php/Download_Pathways here].
|-
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|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{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.

WikiPathways

2008-04-10T00:41:03Z

Apico: edited by Apico via TableEdit

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|
http://www.wikipathways.org
|-
!{{table heading style}} |What:
|
WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.
|-
!{{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:
|
Currently in Beta; new releases every 3 weeks.
|-
!{{table heading style}} |Upcoming events:
|
Manuscript in preparation. Biology Wiki Meeting in the Fall?
|-
!{{table heading style}} |Web Services:
|

|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{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.

WikiPathways

2008-04-10T00:38:30Z

Apico: /* Discussion of {{PAGENAME}} on other websites */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{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.

WikiPathways

2008-04-10T00:15:06Z

Apico: /* Discussion of {{PAGENAME}} on other websites */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{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]

WikiPathways

2008-04-10T00:13:19Z

Apico: /* External Links */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{1|http://www.wikipathways.org}}} {{PAGENAME}}] URL:{{{1|http://www.wikipathways.org}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:12:40Z

Apico: /* References {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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}}==
* Manuscript in preparation

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:12:08Z

Apico: /* Technology {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
* [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 />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:11:54Z

Apico: /* Technology {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==
[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 />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:10:36Z

Apico: /* Other sites with related content {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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===

==Discussion {{HelpIcon|Help:Databases}}==

==References {{HelpIcon|Help:Databases}}==
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:09:59Z

Apico: /* About {{PAGENAME}} {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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.

==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===
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}}==

==Technology {{HelpIcon|Help:Databases}}==
===Web Services/API===

==Discussion {{HelpIcon|Help:Databases}}==

==References {{HelpIcon|Help:Databases}}==
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:07:51Z

Apico: /* Using {{PAGENAME}} {{HelpIcon|Help:Databases}} */

{{Pagetop}}
[[Category:Databases]]
[[Category:Biology wikis]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
|}
</protect>
{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
[{{{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 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 {{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===
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}}==

==Technology {{HelpIcon|Help:Databases}}==
===Web Services/API===

==Discussion {{HelpIcon|Help:Databases}}==

==References {{HelpIcon|Help:Databases}}==
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

WikiPathways

2008-04-10T00:01:36Z

Apico: /* Content {{HelpIcon|Help:Databases}} */

WikiPathways

2008-04-09T23:59:14Z

Apico: /* About {{PAGENAME}} {{HelpIcon|Help:Databases}} */

WikiPathways

2008-04-09T23:58:22Z

Apico: /* About {{PAGENAME}} {{HelpIcon|Help:Databases}} */

WikiPathways

2008-04-09T23:41:27Z

Apico:

WikiPathways

2008-04-09T23:36:56Z

Apico: New page: {{Pagetop}} Category:Databases <protect> <!-- *************************************************************************...

{{Pagetop}}
[[Category:Databases]]

<protect>

{|{{Prettytable}} width='30%' align=right
|-
!{{table heading style}} |Link/URL:
|-
!{{table heading style}} |What:
|-
!{{table heading style}} |Who:
|-
!{{table heading style}} |Updates:
|-
!{{table heading style}} |Upcoming events:
|-
!{{table heading style}} |Web Services:
|-
|colspan='1'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.I47fd53181eb7a&page=0&pagename={{FULLPAGENAMEE}} edit table]
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{{Database_table_help}}
==About {{PAGENAME}} {{HelpIcon|Help:Databases}}==
''Add general information here''
[{{{1|link}}} {{PAGENAME}}] is...
==Content {{HelpIcon|Help:Databases}}==

==Using {{PAGENAME}} {{HelpIcon|Help:Databases}}==
===Browsing===
===Searching===
===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content {{HelpIcon|Help:Databases}}==

==Technology {{HelpIcon|Help:Databases}}==
===Web Services/API===

==Discussion {{HelpIcon|Help:Databases}}==

==References {{HelpIcon|Help:Databases}}==
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}
===Discussion of {{PAGENAME}} on other websites===

Letter to Science about wikifying genome information

2008-04-09T23:24:15Z

Apico: /* signatures */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. David Lipman’s fears that "It would be chaos" are widely shared. These fears need to be balanced, however, by recognition that the expertise of individual curators is unlikely to encompass the collective, albeit intermittently applied, expertise of the larger scientific community (including the 250 signers of the Bidartondo et al. letter). Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki <ref>http://ecoliwiki.net</ref>, the community annotation component of the EcoliHub project <ref>http://ecolihub.org</ref> and GONUTS <ref>http://gowiki.tamu.edu</ref>, a wiki-based browser and annotation engine for Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, but lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist and as part of the study of a specific scientific topic. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to ongoing discussion of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

===signatures===
* James C. Hu, Texas A&M University
* Rodolfo Aramayo, Texas A&M University
* Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
* Christine Elsik, Georgetown University
* Michael Gribskov, Purdue University
* Deborah A. Siegele, Texas A&M University
* Barry L. Wanner, Biological Sciences, Purdue University, West Lafayette, IN 47907
* Alexander R. Pico, The Gladstone Institutes, San Francisco
<references/>

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