WikiNetworks: translating manually created biological pathways for topological analysis

Summary: WikiPathways is a database of 2979 biological pathways across 31 species created using the drawing software PathVisio. Many of these pathways are not directly usable for network-based topological analyses due to differences in curation styles and drawings. We developed the WikiNetworks package to standardize and construct directed networks by combining geometric information and manual annotations from WikiPathways. WikiNetworks performs significantly better than existing tools. This enables the use of high-quality WikiPathways resource for network-based topological analysis of high-throughput data.

Availability and implementation: WikiNetworks is written in Python3 and is available on github.com/Thakar-Lab/wikinetworks and on PyPI.

Supplementary information: Supplementary data are available at Bioinformatics online.