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InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
Breuer, Karin Foroushani, Amir K. Laird, Matthew R Chen, Carol Sribnaia, Anastasia Lo, Raymond Winsor, Geoffrey L Hancock, Robert E.W. Brinkman, Fiona S. L. Lynn, David J
Breuer, Karin
Foroushani, Amir K.
Laird, Matthew R
Chen, Carol
Sribnaia, Anastasia
Lo, Raymond
Winsor, Geoffrey L
Hancock, Robert E.W.
Brinkman, Fiona S. L.
Lynn, David J
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2012-11-24
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Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, and David J. Lynn. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation. Nucl. Acids Res. (2013) 41(D1): D1228-D1233 doi:10.1093/nar/gks1147
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.