EMP observation tables, metadata, and other data and results are available from the Zenodo archive for the Nature paper, the FTP site, and the Qiita EMP Portal.
Content on the FTP site includes:

  • README file describing repository
  • Markdown file describing mapping files and subsets of dataset
  • Flowchart for choosing the best BIOM table for your analyses
  • EMP Sample Type Ontology (EMPO) text file
  • Mapping files
  • OTU observation┬átables
  • OTU information: sequences and trees
  • OTU distribution tables
  • Results: alpha- and beta-diversity


EMP samples and other samples in the Qiita database can be searched by observation data and sample metadata using Redbiom.


Instructions for using the EMP dataset and code for reproducing portions of the EMP meta-analysis are on our GitHub page.