WikiPathways: capturing the full diversity of pathway knowledge

Abstract

WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access.

Figure 1.

Human gene coverage in WikiPathways. (A) Taking KEGG as the gold standard for pathway databases, we plot the growth of WikiPathway (WP) coverage over the past 4 years. WikiPathways shows a relative trend of higher growth. Last year the absolute coverage matched that of KEGG and continues to climb. (B) In terms of gene-for-gene coverage, WikiPathways covers the bulk of the content found in KEGG's canonical pathways (overlap). The proportional Venn diagram also shows that a third of our content is unique. WikiPathways and KEGG unique human gene counts were made by extracting identifiers from archived databases and unifying to Ensembl release 80.

Figure 2.

TissueAnalyzer. Select one of ∼30 tissues from the pulldown list at the top of the page. TissueAnalyzer will then generate a table of pathways based on their selective overrepresentation of active genes in the selected tissue. Select a pathway from the table to open an interactive, web-embedded view with a tissue expression data overlay.

Figure 3.

The new Quick Edit feature. At the base of the interactive pathway view, a series of quick access tabs allow editing of DataNode annotations and properties. The annotation tab provides a DataNode search feature, plus manual override options for type, data source, identifier and label. The properties tab (not active here) provides control of DataNode color and label font attributes. The button on the far right will save any changes made and close the Quick Edit set of tabs.