Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

TLDR

Pathway Tools is a production‑quality environment for building Pathway/Genome Databases that integrate genes, proteins, metabolic and regulatory networks of organisms. This article reviews the capabilities of Pathway Tools. The software performs metabolic pathway, hole‑filler, and operon predictions, supports interactive PGDB editing, web publishing, extensive query and visualization, comparative and systems‑biology analyses, and enables PGDB exchange via a peer‑to‑peer registry. Over 800 PGDBs have been created worldwide using Pathway Tools, many of which are curated for key model organisms.

Abstract

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.