WikiPathways
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts. <protect>
| Link/URL: | |
|---|---|
| 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. |
| edit table |
</protect> See Help:Database_table for how to add or edit information in this section of EcoliWiki.
Contents
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:
Technology
Discussion
References
- Manuscript in preparation
External Links
WikiPathways URL:http://www.wikipathways.org
