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

• Current Version:
  • Number: 1.0
  • Date: 2021-03-15
  • Persistent identifier: https://doi:10.1007/s00248-019-01421-8

Dataset Attribution and Usage

• Dataset Title: TMEN Dataset

• Persistent Identifier: https://doi:10.1007/s00248-019-01421-8

• Dataset Contributors:

  • Creators: Yushi Tang and Donghui Wen

• Date of Issue: 2021-03-15

• Publisher: Peking University

• License:

  • Title: Creative Commons Attribution 4.0 International (CC BY 4.0)
  • Specification: https://creativecommons.org/licenses/by/4.0/

• Suggested Citations:

  • Dataset citation:

    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.

Contact Information

• Primary Contact:

  • Name: Yushi Tang
  • Affiliation: Princeton University
  • ORCID ID: 0000-0002-3809-2129
  • Email: [email protected]

• Alternative Contact:

  • Name: Donghui Wen
  • Affiliation: Peking University
  • ORCID ID: 0000-0002-1301-989X
  • Email: [email protected]

• Contributor ORCID IDs (see above)

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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

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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.

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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

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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:

  • Extension: .csv
  • Media type: text/csv
  • Encoding: UTF-8
  • Standard: RFC 4180 (https://tools.ietf.org/html/rfc4180)

• 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:

  • A comma is used as the record separator and CRLF as the line break (per RFC 4180).
  • All string values are enclosed in double quotes (some contain punctuation, but none contain quotation marks)
  • Timestamps follow the ISO 8601 standard (https://www.iso.org/standard/70907.html; see also https://en.wikipedia.org/wiki/ISO_8601).

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:

  • Extension: .csv
  • Media type: text/csv
  • Encoding: UTF-8
  • Standard: RFC 4180 (https://tools.ietf.org/html/rfc4180)

• 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:

  • A comma is used as the record separator and CRLF as the line break (per RFC 4180).
  • All string values are enclosed in double quotes (some contain punctuation, but none contain quotation marks)
  • Timestamps follow the ISO 8601 standard (https://www.iso.org/standard/70907.html; see also https://en.wikipedia.org/wiki/ISO_8601).

Details for: TMEN_DataPackageDescriptor_2021-03-15.json

• Description: Following the Frictionless Data Specs (https://frictionlessdata.io/specs/), this JSON file serves as a "descriptor" to allow one to work with the dataset as a "data package" (https://specs.frictionlessdata.io/data-package/). It contains much the same information as in this README and the accompanying codebook--i.e., thorough metadata, variable details, and comprehensive information on value types--but in a machine-readable format.

• Format:

  • Extension: .json
  • Media type: application/json
  • Encoding: UTF-8
  • Standard: STD 90 (https://tools.ietf.org/html/std90)

• Size: 1.5 MB

• Other encoding details:

  • Generated using the Data Package Creator browser tool (https://create.frictionlessdata.io/), with "Profile" set to "Data Package."

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):

  • Extension: .pdf
  • Media type: application/pdf
  • Standard: ISO 32000 (https://www.iso.org/standard/51502.html; see also https://www.loc.gov/preservation/digital/formats/fdd/fdd000277.shtml)

• Size: 3.2 MB

• Pages: 72

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END OF README