Article

IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project

Miami University, United States of America
PLoS ONE (Impact Factor: 3.23). 07/2012; 7(7):e40151. DOI: 10.1371/journal.pone.0040151
Source: PubMed

ABSTRACT

The Integrated Microbial Genomes and Metagenomes (IMG/M) resource is a data management system that supports the analysis of sequence data from microbial communities in the integrated context of all publicly available draft and complete genomes from the three domains of life as well as a large number of plasmids and viruses. IMG/M currently contains thousands of genomes and metagenome samples with billions of genes. IMG/M-HMP is an IMG/M data mart serving the US National Institutes of Health (NIH) Human Microbiome Project (HMP), focussed on HMP generated metagenome datasets, and is one of the central resources provided from the HMP Data Analysis and Coordination Center (DACC). IMG/M-HMP is available at http://www.hmpdacc-resources.org/imgm_hmp/.

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    • "The Integrated Microbial Genomes and Metagenomes (IMG/M) [38] is a data management system for the comparative analysis of metagenome sequence data. IMG/M-HMP [39] specifically contains metagenome data from the Human Microbiome Project (HMP) [40]. It contains 748 metagenome datasets generated from sequencing samples from different body sites and also, tools for comparative analysis between hosted sequences and user supplied sequences. "
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    • "The Integrated Microbial Genomes and Metagenomes (IMG/M) [43] is a data management system for the comparative analysis of metagenome sequence data. IMG/M-HMP [44] specifically contains metagenome data from the Human Microbiome Project (HMP) [45]. It contains 748 metagenome datasets generated from sequencing samples from 17 different body sites (number of samples from each site are in brackets); anterior nares (94), keratinised gingiva (6), buccal mucosa (122), hard palate (1), retroauricular crease (20), left (2) and right retroauricular crease (5), palatine tonsils (6), saliva (5), throat (7), tongue dorsum (133), sub- (8) and supra-gingival plaques (127), mid-vagina (2), posterior fornix (60), vaginal introitus (3) and stool (147). "
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    Full-text · Article · Dec 2013 · PLoS ONE
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    • "Metagenome and genome data sets in IMG/M-HMP are grouped both by body site category and by taxonomy, while metagenome data sets are also grouped according to the primary body site and human subjects sampled. HMP-specific analysis ‘workflows’ are discussed in (21). "
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