InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

TLDR

InnateDB is an integrated analysis platform specifically designed to enable systems‑level studies of mammalian innate immunity networks, pathways, and genes. This article details recent updates and improvements to the InnateDB database. The authors report enhancements to the platform, including web service access via the Proteomics Standards Initiative Common Query Interface, expanded Gene Ontology analysis for innate immunity, and new network visualization tools. InnateDB now hosts over 196,000 experimentally validated human, mouse, and bovine interactions, 3,000 pathway annotations across all mammalian systems, more than 18,000 manually curated innate immunity interactions, and has begun curating allergy and asthma data while integrating bovine data to become the first comprehensive network analysis platform for this agricultural model organism.

Abstract

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 allergy- and 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.