Open AccessWikiNetworks: translating manually created biological pathways for topological analysis
Author(s) -
Mukta G Palshikar,
Shan P. Hilchey,
Martin S. Zand,
Juilee Thakar
Publication year - 2021
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btab699
Subject(s) - usable , computer science , software , construct (python library) , resource (disambiguation) , quality (philosophy) , biological network , data mining , topology (electrical circuits) , computational biology , world wide web , programming language , biology , computer network , philosophy , epistemology , mathematics , combinatorics
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.