Op-nare120834 1228..1233

InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergyand asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism. INTRODUCTION The innate immune response is a critical branch of immunity, which not only provides a first line of defence against pathogens, but also regulates and shapes subsequent adaptive responses. Innate immunity, however, can also do great harm by driving inappropriate inflammatory cascades. Therefore complex molecular networks are required to regulate innate immunity and maintain appropriate and specific responses to different pathogens, while limiting potential harm from dysregulated inflammation (1–5). The intricate interplay of a multitude of regulatory layers that initiate and coordinate the innate immune response has led to an ever-increasing interest in applying systems-oriented approaches to better understand innate immunity and its modulators (6). InnateDB (publicly accessible at http://www.innatedb. com and mirrored at http://innatedb.teagasc.ie) is a knowledge base and analysis platform that was specifically designed to provide a system-oriented yet user-friendly tool for integrative analyses of the mammalian innate immune response (7).