IPAVS: Integrated Pathway Resources, Analysis, and Visualization System

Abstract

IPAVS is an integrated knowledgebase that offers biologists a single point of access to several manually-curated pathway resources along with its own expert-curated pathways. IPAVS currently integrates over 500 human pathways (consisting of 25,000 interactions) and mainly includes metabolic pathways, signaling pathways, disease pathways and several large processes maps curated using CellDesinger software. Systems Biology Graphical Notations (SBGN) and KEGG pathway notations are used for the visual display of pathway information. IPAVS also provides a web-based interface that: 1) allows biologists to browse and search pathway resources; 2) provides tools for data import, management (filter, group), and comparisons; 3) offers intuitive visualization and variety of enrichment analysis methods to support the interpretation of biological data in light of cellular processes; and 4) offers basic features for community participation and collaboration. IPAVS can export pathways into variety of standard data formats such as SBML, BioPax and XGMML that can be readily imported and worked with modeling and simulation, or network analysis and visualization software tools. IPAVS enables biologists to do systems biology and employ systems methodologies in their day to day research and produce testable hypothesis. IPAVS is freely accessible at http://ipavs.cidms.org.(Supported by Korea MEST NRF grant (2011-0002144), the 2011 GIST Systems Biology Infrastructure Establishment Grant and KISTI-KREONET).