The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics

We report here the construction, features, and utilization of a comprehensive integrated and non-redundant pathway resource, the NCATS BioPlanet (Figure 1). The resource hosts information only from public sources that have been herein further manually curated to ensure the quality of the data. Along with our pathway warehouse, the NCATS BioPlanet software platform allows easy browsing and visualization of the universe of pathways, and exploration of associations among them. Additionally, we curated the set of annotated pathways in terms of the biological space covered and the current availability of assays, either commercial or academic, to probe each subspace. After eliminating redundancy across the pathway databases used to create the BioPlanet, we found that human cells incorporate 1,658 pathways. Starting with these pathways, we utilized a condensation approach to construct a minimal set of assays to cover all of pathway space. This minimal set of pathways will serve as the starting point to prioritize pathways for testing in a wide variety of systems biology efforts, and provides a reduced-complexity set for the systems pharmacology community. The NCATS BioPlanet will be continually updated and is publicly accessible at http://tripod.nih.gov/bioplanet/. FIGURE 1 Figure 1. Workflow for the NCATS BioPlanet construction process. Data, Methods, and Results Source Databases Annotations for pathways and gene-gene or protein–protein interactions were o...
Source: Frontiers in Pharmacology - Category: Drugs & Pharmacology Source Type: research