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

By 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, D. Lynn. Nucleic Acids Res., 2012

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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.

Subfields: Immunology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/07b66f61fc3425a02cae661a387972e04d994cba

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Citations in the corpus

The BioGRID interaction database: 2019 update (2018, background): “Other major meta-database resources that disseminate BioGRID data include STRING (32), Pathway Commons (31), Gene Mania (89), InnateDB (90) and FlyAtlas (91) (see https://wiki.thebiogrid.org/doku.php/partners for full list).”
NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration (2014, methodology): “NetworkAnalyst uses a comprehensive high-quality PPI database downloaded from the InnateDB (19), which participates in the International Molecular Exchange (IMEx) consortium (20).”
Integrated interactions database: tissue-specific view of the human and model organism interactomes (2015, neutral): “3, InnateDB (18) 2015-05-23, IntAct (15) 2015-06-13 and MINT (16) 2013-03-26.”
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data (2015, methodology): “Make sure that the ‘InnateDB Interactome’ and ‘Data1’ are selected, and click the ‘OK’ button to proceed to the next page.”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, methodology): “In total, 11 molecular interaction databases (including IntAct) were incorporated into IntAct including AgBase [ 266–269], MINT [ 270–273], UniProt [274][41], I2D [275], MBINFO, MatrixDB [276], Molecular Connections, InnateDN [ 277], IMEx [278] and GOA.”
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases (2013, background): “…I2D (Interologous Interaction Database) (20), which curates interaction protein interaction data relevant to the development of cancer and InnateDB (21), capturing both protein and gene interactions relevant to the process of innate immunity, choose to select appropriate records directly from the…”
Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation (2014, methodology): “We confirmed our approaches by interrogating these gene sets with the GO analysis, pathway analysis, and transcription factor (TF) binding prediction tools provided by InnateDB, with the same outcome (Tables S2C–S2K).”