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

Karin Breuer, Amir Foroushani, Matthew Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey Winsor, Robert Hancock, Fiona Brinkman, David Lynn

    Research output: Contribution to journalArticlepeer-review

    564 Citations (Scopus)

    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 >196000 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 18000 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.

    Original languageEnglish
    Pages (from-to)D1228-D1233
    Number of pages1
    JournalNucleic Acids Research
    Volume41
    Issue numberD1
    DOIs
    Publication statusPublished - 1 Jan 2013

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