human-microbiome-project.yaml

Name: The Human Microbiome Project
Description: The NIH-funded Human Microbiome Project (HMP) is a collaborative effort of over 300 scientists from more than 80 organizations to comprehensively characterize the microbial communities inhabiting the human body and elucidate their role in human health and disease. To accomplish this task, microbial community samples were isolated from a cohort of 300 healthy adult human subjects at 18 specific sites within five regions of the body (oral cavity, airways, urogenital track, skin, and gut). Targeted sequencing of the 16S bacterial marker gene and/or whole metagenome shotgun sequencing was performed for thousands of these samples. In addition, whole genome sequences were generated for isolate strains collected from human body sites to act as reference organisms for analysis. Finally, 16S marker and whole metagenome sequencing was also done on additional samples from people suffering from several disease conditions.
Documentation: https://commonfund.nih.gov/hmp
Contact: https://commonfund.nih.gov/hmp/related_activities
UpdateFrequency: Uncertain
Tags:
  - aws-pds
  - life sciences
  - genetic
  - genomic
  - metagenomics
  - microbiome
  - fasta
  - amino acid
  - fastq
License: The data is publicly available to the community free of charge.
Resources:
  - Description: https://aws.amazon.com/datasets/human-microbiome-project/
    ARN: arn:aws:s3:::human-microbiome-project
    Region: us-west-2
    Type: S3 Bucket
DataAtWork:
  Tutorials:
  Tools & Applications:
  Publications:
    - Title: Strains, functions and dynamics in the expanded Human Microbiome Project
      URL: https://www.nature.com/articles/nature23889
      AuthorName: Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
    - Title: The Human Microbiome Project
      URL: https://www.nature.com/articles/nature06244
      AuthorName: Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
    - Title: New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract
      URL: https://www.sciencedirect.com/science/article/pii/S2452231718300289
      AuthorName: Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al