GMrepo: a database of curated and consistently annotated human gut metagenomes

Abstract GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial...

Full description

Saved in:
Bibliographic Details
Published inNucleic acids research Vol. 48; no. D1; pp. D545 - D553
Main Authors Wu, Sicheng, Sun, Chuqing, Li, Yanze, Wang, Teng, Jia, Longhao, Lai, Senying, Yang, Yaling, Luo, Pengyu, Dai, Die, Yang, Yong-Qing, Luo, Qibin, Gao, Na L, Ning, Kang, He, Li-jie, Zhao, Xing-Ming, Chen, Wei-Hua
Format Journal Article
LanguageEnglish
Published England Oxford University Press 08.01.2020
Subjects
Database Issue
Databases, Genetic
Gastrointestinal Microbiome
Genes, Bacterial
Genome, Human
Humans
Metagenome
Metagenomics - methods
Molecular Sequence Annotation
Software
Online AccessGet full text

Cover

More Information
Summary:Abstract GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries. For example, to find (1) samples from healthy individuals of 18 to 25 years old with BMIs between 18.5 and 24.9, or (2) projects that are related to colorectal neoplasms, with each containing >100 samples and both patients and healthy controls. Precomputed species/genus relative abundances, prevalence within and across phenotypes, and pairwise co-occurrence information are all available at the website and accessible through programmable interfaces. So far, GMrepo contains 58 903 human gut samples/runs (including 17 618 metagenomes and 41 285 amplicons) from 253 projects concerning 92 phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz764