How to make a pathway

Creating biological pathways for WikiPathways using PathVisio

Authors: Friederike Ehrhart, Martina Summer-Kutmon, Egon Willighagen, Kristina Hanspers, Alexander Pico, Linda Rieswijk (Maastricht University), Penny Nymark (MIsvik Biology)


This tutorial shows users how to make a biological (or biochemical) pathway for WikiPathways using the software PathVisio. The information and images are derived from help pages of WikiPathways with some recent updates. Pathways can be created from e.g. comprehensive images in reviews showing the interactions of genes, proteins and metabolites in a good graphical way. Pathways can show molecular biological interactions like signal cascades, enzyme reactions, transport mechanisms of “healthy” pathways, drug or nanoparticle interactions, adverse outcome pathways and diseases.

You can find examples for nanomaterial specific pathways and discussions in the nanomaterials portal of WikiPathways.

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 collaborative 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, WikiPathways added a custom graphical pathway editing tool and integrated identifier 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.

You can download the tutorial >> here << or see it in the preview window below.