MicrobiomeDB: a Systems Biology Platform for Integrating, Mining and Analyzing Microbiome Experiments

Francislon S. Oliveira,John Brestelli,Shon Cade,Jie Zheng,John Iodice,Steve Fischer,Cristina Aurrecoechea,Jessica C. Kissinger,Brian P. Brunk,Christian J. Stoeckert,Gabriel R. Fernandes,David S. Roos,Daniel P. Beiting

Nucleic Acids Research（2017）SCI 2区

FIOCRUZ Minas | Univ Penn | Univ Georgia

Cited 46|Views96

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.

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Human Metabolome Database

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Pretraining has recently greatly promoted the development of natural language processing (NLP)
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