MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

• Published in: Nucleic acids research Vol. 46; no. D1; pp. D684 - D691
• Main Authors: Oliveira, Francislon S, Brestelli, John, Cade, Shon, Zheng, Jie, Iodice, John, Fischer, Steve, Aurrecoechea, Cristina, Kissinger, Jessica C, Brunk, Brian P, Stoeckert, Christian J, Fernandes, Gabriel R, Roos, David S, Beiting, Daniel P
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.01.2018
• Subjects: Animals; Computer Simulation; Data Mining - methods; Database Issue; Databases, Genetic; Datasets as Topic; Environmental Microbiology; Genetic Variation; Humans; Internet; Microbiota; Mobile Applications; Systems Biology; User-Computer Interface; Workflow
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkx1027

Abstract MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate.