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

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...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943048/
https://www.ncbi.nlm.nih.gov/pubmed/31504765
http://dx.doi.org/10.1093/nar/gkz764
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author 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
author_facet 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
author_sort Wu, Sicheng
collection PubMed
description 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.
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spelling pubmed-69430482020-01-08 GMrepo: a database of curated and consistently annotated human gut metagenomes 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 Nucleic Acids Res Database Issue 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. Oxford University Press 2020-01-08 2019-09-04 /pmc/articles/PMC6943048/ /pubmed/31504765 http://dx.doi.org/10.1093/nar/gkz764 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
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
GMrepo: a database of curated and consistently annotated human gut metagenomes
title GMrepo: a database of curated and consistently annotated human gut metagenomes
title_full GMrepo: a database of curated and consistently annotated human gut metagenomes
title_fullStr GMrepo: a database of curated and consistently annotated human gut metagenomes
title_full_unstemmed GMrepo: a database of curated and consistently annotated human gut metagenomes
title_short GMrepo: a database of curated and consistently annotated human gut metagenomes
title_sort gmrepo: a database of curated and consistently annotated human gut metagenomes
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943048/
https://www.ncbi.nlm.nih.gov/pubmed/31504765
http://dx.doi.org/10.1093/nar/gkz764
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