About InnateDB

[Array logo]InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation. Our curation team systematically reviews and curates experimentally-validated human and mouse interactions from the biomedical literature. Bovine interactions are largely predicted via orthology with these interaction participants. Human and mouse interactions are curated with rich contextual annotations including information on the participant molecules, the reference publication, the interaction detection method, the cell and tissue types in which the interaction was described and a variety of other information in compliance with the recently proposed minimum information for molecular interactions (MIMIx) standard (Nat. Biotech., 2007). We have developed the InnateDB submission system to allow curators to submit data using a structured controlled vocabulary for the annotation of protein-protein interaction experiments (Developed by the HUPO Proteomics Standards Initiative). For further details on InnateDB curation please refer to our paper describing InnateDB curation of the innate immunity interactome which has been published in BMC Systems Biology.

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InnateDB is a member of the International Molecular Exchange Consortium (IMEx). This organization is dedicated to developing rules for capturing protein-protein interaction data, actively curating these interactions from the scientific literature and making them available through a common website.

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If you use this database, please cite the following publication

Breuer et al., InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucl. Acids Res. (2013) 41 (D1)  PDF Icon

Other relevant publications

Frias et al., CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database 2015; May 7  PDF Icon
Lynn et al., InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology 2008; 4:218  PDF Icon
Lynn et al., Curating the Innate Immunity Interactome. BMC Systems Biology 2010; 4:117. PDF Icon