WikiPathways: Difference between revisions

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{{Wiki
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|founder         = [https://www.WikiPathways.org/index.php/User:Thomas Thomas Kelder]
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'''WikiPathways''' is a {{tag|database}} of biological pathways maintained by and for the {{tag|Science|scientific}} community.
{{Cquote|
;''What is WikiPathways
'''WikiPathways''' was established to facilitate the contribution and maintenance of pathway information by the {{tag|biology}} community.  WikiPathways is an open, {{tag|Collaboration|collaborative}} platform dedicated to the {{tag|curation}} of biological pathways.  WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as [https://www.Genome.jp/kegg/ KEGG], [https://Reactome.org Reactome] and [https://www.PathwayCommons.org Pathway Commons].  Building on the same {{tag|MediaWiki}} software that powers [[:Category:Wikipedia|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 {{tag|student}}s to senior experts in each field.  This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
;''Why Pathways
Biological pathways provide intuitive views of the myriad of interactions underlying biological processes.  A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows.  These powerful representations are essential tools, common among the [[:Category:Textbooks|textbooks]] and review articles that document any given field of biology.  Making these tools available for computational methods of analysis will allow {{tag|research}}ers to connect pathways to databases of biological annotations and experimental {{tag|data}}, creating effective products of systems biology.  Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.
;''How Does it Work
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.  [[User]]s can easily monitor and [[undo]] changes, compare [[diff]]erences 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.  ''We are adding new features all the time.  Visit the [https://www.WikiPathways.org/index.php/Help:Contents Help pages] to learn how to use the latest features.''|author=WikiPathways wiki site, ({{tag|Wiki Creative Commons Public Domain Dedication (CC0)|CC0}})|source=https://www.WikiPathways.org/index.php/WikiPathways:About}}
;''{{tag|GreatFeature|Great features}}
*WikiPathways wiki has its own unique customised statistics page.  This offers a weighted table of [[user]] contribution 'scores', a custom 'page count' specifically for their 'pathways' (in a similar vein that we list commons wikis by their number of [[file]]s rather than article pages), plus a number of visual graphs displaying various metrics of the WikiPathways wiki site;
*Every month, WikiPathways releases its latest curated updated [https://www.wikipathways.org/index.php/Download_Pathways Pathways for download]
;''External links
*[https://www.WikiPathways.org/index.php/Special:BrowsePathways Special: BrowsePathways] — all available Pathways available on the WikiPathways wiki site
*[https://WikiPathways-Data.WMCloud.org WikiPathways data downloads] — hosted by [[:Category:Wikimedia Cloud Services|Wikimedia Cloud Services]], at WikiPathways-Data.WMCloud.org
{{WikiApiary}}
*[https://new.WikiPathways.org/academy/ WikiPathways Academy] — organized training examples for new WikiPathways authors, at new.WikiPathways.org
*[https://PathVisio.org PathVisio] — free open-source pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways for WikiPathways
*[[GitHub:wikipathways|WikiPathways]] — open source software development related to the WikiPathways project, at [[GitHub|GitHub.com]]
*[[GitHub:wikipathways/wikipathways.org|WikiPathways.org]] — main (current) repository for the WikiPathways project, at GitHub.com
*[[GitHub:wikipathways/SARS-CoV-2-WikiPathways|SARS-CoV-2 WikiPathways]] — temporary repository of RDF of selected pathways for SARS-CoV-2 (the virus which caused the Coronavirus Covid-19 pandemic) from WikiPathways, supporting the [[:Category:Wikidata|Wikidata]] bot, at GitHub.com
*[https://Twitter.com/WikiPathways @WikiPathways] — official Twitter feed
*[[GitHub:gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-Pathway-Modeling|Introduction to Pathway Modeling for Biologists]] — at GitHub.com


'''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.
[[Category:FoundedIn2007]]<!--https://www.WikiPathways.org/index.php?title=WikiPathways&dir=prev&action=history-->

Revision as of 23:36, 11 August 2022

https://www.WikiPathways.org/skins/common/images/wplogo_125.png WikiPathways
Recent changes
[No WikiNode]
About
[No Mobile URL]
Founded by: Thomas Kelder
Status: Vibrant
Language: English
Edit mode: LoginToEdit
Wiki engine: MediaWiki
Wiki license: Creative Commons Public Domain Dedication (CC0)
Main topic: Biology
Wiki size: 3,085 article pages see stats
wikiFactor: 17 info / verify

(As of: 2022-08-11)


WikiPathways is a database of biological pathways maintained by and for the scientific community.

What is 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.

Why Pathways

Biological pathways provide intuitive views of the myriad of interactions underlying biological processes. A typical signaling pathway, for example, can represent receptor-binding events, protein complexes, phosphorylation reactions, translocations and transcriptional regulation, with only a minimal set of symbols, lines and arrows. These powerful representations are essential tools, common among the textbooks and review articles that document any given field of biology. Making these tools available for computational methods of analysis will allow researchers to connect pathways to databases of biological annotations and experimental data, creating effective products of systems biology. Collecting and maintaining pathway information in a robust database, however, is an ongoing challenge.

How Does it Work

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. We are adding new features all the time. Visit the Help pages to learn how to use the latest features.

 — WikiPathways wiki site, (CC0), https://www.WikiPathways.org/index.php/WikiPathways:About

Great features
  • WikiPathways wiki has its own unique customised statistics page. This offers a weighted table of user contribution 'scores', a custom 'page count' specifically for their 'pathways' (in a similar vein that we list commons wikis by their number of files rather than article pages), plus a number of visual graphs displaying various metrics of the WikiPathways wiki site;
  • Every month, WikiPathways releases its latest curated updated Pathways for download
External links
Retrieved from "https://wikiindex.org/index.php?title=WikiPathways&oldid=222159"