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Updated: May 27, 2025
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
AOP-networkFinder-a versatile tool for the reconstruction and visualization of Adverse Outcome Pathway networks from
Nurettin Yarar1,2, Marvin Martens3, Torbjørn Rognes1,4
1Department of Informatics, University of Oslo, Oslo 0373, Norway.
Motivation:
The Adverse Outcome Pathways (AOP)-Wiki, a knowledge database for AOPs, requires an efficient way to present an overview of its content for the reconstruction of networks by experts in a given domain. We have developed the AOP-networkFinder, a user-friendly tool that retrieves AOPs of interest, allows network generation and cleaning, and finally visualizes networks built around the retrieved AOPs. Our tool constructs AOP networks by connecting AOPs that use the same Key Events (KEs) in a versatile but controlled manner. Genes related to these KEs are also displayed. The constructed networks can then be exported as images or to Cytoscape for further fine-tuning and statistical analysis.
Results:
The AOP-networkFinder allows users to comprehensively identify relationships between KEs and visualize the overall structure of an AOP both quickly and easily. This is immensely beneficial to researchers who need to understand the complex interplay between different KEs and the overall pathway they are studying and helps them to build further networks of interest while logging relevant information about changes within the network. These efforts are in line with the Findable, Accessible, Interoperable, and Reusable principles, which are crucial attributes for any developed databases and tools for optimizing (re)use in a dynamically changing landscape of AOP-Wiki.
Availability And Implementation:
The AOP-networkFinder is an open-source application and is available online at aop-networkfinder.no, in the 'Computational Toxicology at Norwegian Institute of Public Health' Zenodo community at DOI 10.5281/zenodo.11068434, in the GitHub repository at github.com/folkehelseinstituttet/AOPnetworkFinder_v1, as well as in a Docker image at hub.docker.com/r/nurre123/aop_network_finder. The software is available under the GNU Affero General Public License (AGPL), v3.0. The tool uses the AOP-Wiki SPARQL endpoint to retrieve AOP data.
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