WikiPathways 2024: next generation pathway database

Abstract

WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing and curating pathway knowledge, thus providing stability for the future of community pathway curation. The website has been redesigned to improve and enhance user experience. This next generation of WikiPathways continues to support existing features while improving maintainability of the database and facilitating community input by providing new functionality and leveraging automation.

Graphical Abstract

Figure 1.

Recent growth of WikiPathways. The bar plot shows the total number of monthly edits, the line plot shows the total number of pathways in WikiPathways, and the x-axis is years. A dynamically updated version of this plot is available on the front page of the WikiPathways website. Note that the pathway count only includes human-curated content that has been reviewed and merged into the WikiPathways database; we are not counting inferred, converted or incomplete pathways.

Figure 2.

Composite screenshots of (A) the new WikiPathways.org home page and new cross-linking features via collections (B) throughout the new site, for example on pathway pages (C). Wherever organisms are mentioned, blue, rounded buttons are consistently used, establishing a visual lexicon and means of navigation. Likewise, green buttons represent our curator communities, and purple buttons signify ontology annotations.

Figure 3.

New pipeline for pathway submission, review, and acceptance. Orange boxes represent pathway author action; blue boxes represent automated steps; green boxes represent tasks performed by human reviewers.

Figure 4.

(A–K) An example of a pathway page on the updated WikiPathways website. Labels A–K highlight the features and interaction options on the page. This interface displays a button to open the model fullscreen (A), download and share the pathway (B), the authors (C), editing history and last activity (D), pathway discussion options (E), publications citing this pathway model (F), organisms relevant for this pathway (G), communities involved in this model (H), disease and pathway ontology annotations (I), participants of this pathway (J) and references to support this model (K).

Figure 5.

Side-by-side of original figure and model. (A) From the original figure (16), identifiable gene names were extracted by the Pathway Figure OCR pipeline, pfocr.wikipathways.org/figures/PMC6143874__etm-16-04-3275-g02.html. (B) The corresponding curated pathway model on WikiPathways, wikipathways.org/instance/WP5358 (17), which can then be used in a variety of downstream analyses and visualizations. The pathway model can be styled in Cytoscape (colors, shapes, labels, graphical annotations) to create a publication-ready pathway figure, for example to recreate the look of the original figure (see the section on Data Analysis and Visualization).