Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways.

WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.

WikiPathways thus presents a new model for 'pathway databases' that enhances and complements ongoing efforts, such as KEGG, Reactome (see G6G Abstract Number 20267) and Pathway Commons (see G6G Abstract Number 20366).

Building on the same MediaWiki software that powers Wikipedia, the manufacturer 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.

Biological 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 advanced 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.

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 (GenMAPP Pathway Markup Language);

which is a custom XML format compatible with pathway visualization and analysis tools such as Cytoscape (see G6G Abstract Number 20092), GenMAPP (see G6G Abstract Number 20219) and PathVisio (see G6G Abstract Number 20243).

WikiPathways Basic Statistics --

There are 1,259 pathways -

Number of pathways (and unique genes) per species:

Note: Although WikiPathways is inspired by the open philosophy of Wikipedia and other wiki's, it is an independent project and Not directly related to Wikipedia or other projects of the Wikimedia foundation.

System Requirements



Manufacturer Web Site WikiPathways

Price Free.

G6G Abstract Number 20367

G6G Manufacturer Number 104016