/TMEN

Tripartite Microbial-Environment Network Analysis

Primary LanguageR

Reference Information

Provenance for this README

  • File name: README_TMEN_Data.txt
  • Author: Yushi Tang
  • Other contributors: Donghui Wen
  • Date created: 2021-03-01
  • Date modified: 2021-03-15

Dataset Version and Release History

Dataset Attribution and Usage

Contact Information

  • Primary Contact:

  • Alternative Contact:

    • Name: Donghui Wen
    • Affiliation: Peking University
    • ORCID ID: 0000-0002-1301-989X
    • Email: dhwen@pku.edu.cn

  • Contributor ORCID IDs (see above)

Additional Dataset Metadata

Acknowledgements

  • Funding source: General Project Nos. 51678003 and 51678334 of Natural Science Foundation

Relations to Other Datasets and/or Publications

  • References for replication code for the dataset and related analyses:
    • Tang, Y., Dai, T., Su, Z. et al. A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. Microb Ecol (2019) https://doi.org/10.1007/s00248-019-01421-8.

Dates and Locations

  • Dates of data collection: start=2015-04-01; end=2015-04-30

  • Geographic locations of data collection: Hangzhou Bay, Zhejiang, PRC

Methodological Information

  • Methods of data collection: The data were collected following the procedures developed by Wen Lab at Peking University, as detailed in Dai, Tianjiao, et al. 2016 https://doi.org/10.1093/femsec/fiw203.

  • Methods of data processing: Raw measurements were compiled into one CSV with minimal processing, as detailed in "TMEN_Codebook_2021-03-15.pdf".

  • Software-specific information: The dataset and codebook do not require any specific software to read and reuse, but the data package follows the Frictionless Data framework, which has libraries for multiple languages: https://frictionlessdata.io/tooling/libraries/#data-package.

Data and File Overview

Summary Metrics

  • File count: 5
  • Total file size: 4.8 MB
  • Range of individual file sizes: 9 KB - 3.2 MB
  • File formats: TXT, CSV, JSON, PDF

Naming Conventions

  • File naming scheme: Each file name has three fields, delimimited by underscores (followed by the file extension):
    1. Project shorthand: "TMEN" in all cases
    2. Content type: "RawData"; "README"; "DataPackageDescriptor"; or "Codebook"
    3. Date of latest revision to the file by the creators

Table of Contents

  • TMEN_README_2021-03-15.txt, 9 KB
  • TMEN_RawData_Bacteria_Species_2021-03-15.csv, 152 KB
  • TMEN_RawData_Archaea_Species_2021-03-15.csv, 22 KB
  • TMEN_DataPackageDescriptor_2021-03-15.json, 1.5 MB
  • TMEN_Codebook_2021-03-15.pdf, 3.2 MB

File Details

Details for: README_2021-03-15.txt

  • Description: This is the README file you are reading right now--the introduction to the dataset and accompanying documentation files.

  • Format:

    • Extension: .txt
    • Media type: text/plain
    • Encoding: UTF-8

  • Size: 9 KB

Details for: TMEN_RawData_Bacteria_Species_2021-03-15.csv

  • Description: This file represents the dataset itself; all other files are documentation for the dataset.

  • Format:

  • Size: 152 KB

  • Dimensions: 1406 rows; 36 columns

  • Variables:

    • The first line contains variable names as column headers.
    • The full details on all variables, including naming schemes, descriptions and value types, are contained in the data package and the codebook.

  • Missing data codes: Missing values are left blank in all cases.

  • Other encoding details:

Details for: TMEN_RawData_Archaea_Species_2021-03-15.csv

  • Description: This file represents the dataset itself; all other files are documentation for the dataset.

  • Format:

  • Size: 22 KB

  • Dimensions: 168 rows; 36 columns

  • Variables:

    • The first line contains variable names as column headers.
    • The full details on all variables, including naming schemes, descriptions and value types, are contained in the data package and the codebook.

  • Missing data codes: Missing values are left blank in all cases.

  • Other encoding details:

Details for: TMEN_DataPackageDescriptor_2021-03-15.json

Details for: TMEN_Codebook_2021-03-15.pdf

  • Description: This codebook provides comphrensive documentation for the all of the variables and values in the dataset in a human-readable form. This includes variable naming schemes, labels and descriptions for all variables (including some descriptive statistics), as well as details on all value types and units of measurement.

  • Format(s):

  • Size: 3.2 MB

  • Pages: 72

END OF README