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

2019 Nucleic Acids Research  
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes.  ...  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.  ...  CONCLUSIONS In this study, we introduced GMrepo, an online database of curated, consistently annotated meta-data and human gut metagenomic data.  ... 
doi:10.1093/nar/gkz764 pmid:31504765 pmcid:PMC6943048 fatcat:7dq5yavtgzfc5ewbqpoxg3464i

mAML: an automated machine learning pipeline with a microbiome repository for human disease classification

Fenglong Yang, Quan Zou
2020 Database: The Journal of Biological Databases and Curation  
GMrepo database.  ...  In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the  ...  GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomic data, which contains 58 903 human gut samples/runs, including 17 618 metagenomes and  ... 
doi:10.1093/database/baaa050 pmid:32588040 pmcid:PMC7316531 fatcat:3ja4eunjabbnvmirgcs2ptyfoa

mAML: an automated machine learning pipeline with a microbiome repository for human disease classification [article]

Fenglong Yang, Quan Zou
2020 bioRxiv   pre-print
GMrepo database.  ...  In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the  ...  GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomic data, which contains 58903 human gut author/funder. All rights reserved.  ... 
doi:10.1101/2020.02.11.943316 fatcat:nyuepitddnfopgm6t63x4thtwa

mBodyMap: a curated database for microbes across human body and their associations with health and diseases

Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen
2021 Nucleic Acids Research  
mBodyMap is a curated database for microbes across the human body and their associations with health and diseases.  ...  Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of  ...  tions on using R and Python to access our data can be found at the 'Programmable access' section of the 'Help' page or our GitHub page: https://github.com/whchenlab/ mBodymap/tree/main/programmable-access  ... 
doi:10.1093/nar/gkab973 pmid:34718713 pmcid:PMC8728210 fatcat:2ebsb24c4bgzddr7ybj2dt625m

gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites

Liang Cheng, Changlu Qi, Haixiu Yang, Minke Lu, Yiting Cai, Tongze Fu, Jialiang Ren, Qu Jin, Xue Zhang
2021 Nucleic Acids Research  
gutMGene (http://bio-annotation.cn/gutmgene), a manually curated database, aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice.  ...  The current version of gutMGene documents 1331 curated relationships between 332 gut microbes, 207 microbial metabolites and 223 genes in humans, and 2349 curated relationships between 209 gut microbes  ...  For example, GMrepo (19) and gutMEGA (20) curated and annotated human gut metagenomes. gutMDisorder (21) collected experimentally validated associations between gut microbiota and diseases or intervention  ... 
doi:10.1093/nar/gkab786 pmid:34500458 pmcid:PMC8728193 fatcat:x7fryh2drrgczpjoq77sspyqjm

Gut microbiota imbalance in colorectal cancer patients, the risk factor of COVID-19 mortality

Changjing Cai, Xiangyang Zhang, Yihan Liu, Edward Shen, Ziyang Feng, Cao Guo, Ying Han, Yanhong Ouyang, Hong Shen
2021 Gut Pathogens  
Results Based on the GMrepo database, the gut microbiota of 1374 patients with colorectal neoplasms and 27,329 healthy people was analyzed to investigate the differences in the abundance of microbes between  ...  Conclusions Our work draws an initial point that gut microbiota imbalance is a risk factor of COVID-19 mortality and gut microbiota may provide a new therapeutic avenue for colorectal cancer patients.  ...  Methods Dataset source and preprocessing GMrepo database GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes.  ... 
doi:10.1186/s13099-021-00466-w pmid:34863291 pmcid:PMC8643189 fatcat:l4nk6jh6mbe6vhv7az25zwq5ga

Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

Gongchao Jing, Lu Liu, Zengbin Wang, Yufeng Zhang, Li Qian, Chunxiao Gao, Meng Zhang, Min Li, Zhenkun Zhang, Xiaohan Liu, Jian Xu, Xiaoquan Su (+1 others)
2021 mSystems  
MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata  ...  of a whole microbiome to those in the database.  ...  X.S. acknowledges the support of grants 31771463 and 32070086 from the National Natural Science Foundation of China.  ... 
doi:10.1128/msystems.00943-20 pmid:33468706 fatcat:larqtlsqkngv7bzoulyyyjowc4

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

Giulia Agostinetto, Davide Bozzi, Danilo Porro, Maurizio Casiraghi, Massimo Labra, Antonia Bruno
2022 Database: The Journal of Biological Databases and Curation  
Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.  ...  Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them.  ...  In addition, important field-specific databases were created, such as the Human Oral Microbiome Database (35) or the GMrepo, a database of curated and consistently annotated human gut metagenomes (36  ... 
doi:10.1093/database/baac033 pmid:35576001 fatcat:osiz6ic7hjg3zhvcq53hcqmzba

Enabling technology for microbial source tracking based on transfer learning: From ontology-aware general knowledge to context-aware expert systems [article]

Kang Ning, Hui Chong, Qingyang Yu, Yuguo Zha, Guangzhou Xiong, Nan Wang
2021 bioRxiv   pre-print
For example, when dealing with 650 samples from a recent study of colorectal cancer, EXPERT could achieve an AUROC of 0.95 when predicting the host's phenotypical status.  ...  source tracking: diverse and context-dependent applications are asking for quantification of the contributions of different niches (biomes), which have already overwhelmed existing methods.  ...  GMrepo: a database of curated and consistently annotated human gut Pathmanathan, J. S., Lannes, R., Lopez, P. & Bapteste, E.  ... 
doi:10.1101/2021.01.29.428751 fatcat:6v4gtuphondobmd4k5enkvbfo4