ESS-DIVE Reporting Format for Amplicon Abundance Table

Weisenhorn, Pamela; Beilsmith, Kathleen

doi:10.15485/1865729

Title: ESS-DIVE Reporting Format for Amplicon Abundance Table

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Abstract

While standardized sequencing data is available in public repositories and efforts such as MIxS for common sample collection and processing metadata are well established, the lack of common bioinformatic processing metadata has hindered the ability to do large-scale metaanalyses and the potential for data re-use by non-experts such as ecosystem, watershed, or earth system modelers. To address this need for Department of Energy researchers, we have developed an amplicon reporting format which captures both sample preparation and bioinformatic processing metadata and stores processed amplicon data as a paired abundance table and sequencing file to maximize the potential for re-use of these data. To aid in the adoption of accessible and reproducible analysis workflows, this reporting format was developed in concert with amplicon functionality within the Department of Energy’s Systems Biology Knowledgebase (KBase) to ensure common data and metadata requirements and facilitate seamless transfer between these platforms.This dataset contains support documentation for the amplicon reporting format (README.md and instructions.md), templates for both bioinformatic and sequencing metadata (amplicon_bioinformatic_metadata_template_2021_10_03.csv and amplicon_sequencing_metadata_template_2021_10_03.csv), a crosswalk indicating how this reporting format relates to the current MIxS format (ESSDIVE-MIxS_crosswalk.csv), a list of available instrument terms (amplicon_seq_instrument_terms_2021_10_03.csv), a map between QIIME2 parameter settings and metadata fields (amplicon_qiime2_plugin_metadata_map.csv), amore »« less

Authors:

;

Argonne National Laboratory; Argonne National Laboratory
Argonne National Laboratory

Publication Date:: Sat Jan 01 04:00:00 UTC 2022

Other Number(s):: https://doi.org/10.15485/1865729

Research Org.:: Environmental System Science Data Infrastructure for a Virtual Ecosystem; Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)

Sponsoring Org.:: U.S. DOE > Office of Science > Biological and Environmental Research (BER)

Subject:: 54 ENVIRONMENTAL SCIENCES; Earth Science > Biosphere > Ecological Dynamics; Earth Science > Biosphere > Ecological Dynamics > Community Dynamics > Community Structure; Earth Science > Biosphere > Ecological Dynamics > Community Dynamics > Indicator Species; Earth Science > Biosphere > Ecological Dynamics > Species/Population Interactions > Microbial Changes

OSTI Identifier:: 1865729

DOI:: https://doi.org/10.15485/1865729

Citation Formats


                    Weisenhorn, Pamela, and Beilsmith, Kathleen. ESS-DIVE Reporting Format for Amplicon Abundance Table.  United States: N. p., 2022. 
        Web.  doi:10.15485/1865729.

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                    Weisenhorn, Pamela, & Beilsmith, Kathleen. ESS-DIVE Reporting Format for Amplicon Abundance Table.  United States.  doi:https://doi.org/10.15485/1865729

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                    Weisenhorn, Pamela, and Beilsmith, Kathleen. 2022.  
"ESS-DIVE Reporting Format for Amplicon Abundance Table".  United States.  doi:https://doi.org/10.15485/1865729.  https://www.osti.gov/servlets/purl/1865729. Pub date:Sat Jan 01 04:00:00 UTC 2022

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@article{osti_1865729,

  title        = {ESS-DIVE Reporting Format for Amplicon Abundance Table},

  author       = {Weisenhorn, Pamela and Beilsmith, Kathleen},

  abstractNote = {While standardized sequencing data is available in public repositories and efforts such as MIxS for common sample collection and processing metadata are well established, the lack of common bioinformatic processing metadata has hindered the ability to do large-scale metaanalyses and the potential for data re-use by non-experts such as ecosystem, watershed, or earth system modelers. To address this need for Department of Energy researchers, we have developed an amplicon reporting format which captures both sample preparation and bioinformatic processing metadata and stores processed amplicon data as a paired abundance table and sequencing file to maximize the potential for re-use of these data. To aid in the adoption of accessible and reproducible analysis workflows, this reporting format was developed in concert with amplicon functionality within the Department of Energy’s Systems Biology Knowledgebase (KBase) to ensure common data and metadata requirements and facilitate seamless transfer between these platforms.This dataset contains support documentation for the amplicon reporting format (README.md and instructions.md), templates for both bioinformatic and sequencing metadata (amplicon_bioinformatic_metadata_template_2021_10_03.csv and amplicon_sequencing_metadata_template_2021_10_03.csv), a crosswalk indicating how this reporting format relates to the current MIxS format (ESSDIVE-MIxS_crosswalk.csv), a list of available instrument terms (amplicon_seq_instrument_terms_2021_10_03.csv), a map between QIIME2 parameter settings and metadata fields (amplicon_qiime2_plugin_metadata_map.csv), a data dictionary (amplicon_CSV_dd.csv), and file-level metadata (amplicon_FLMD.csv).},

  doi          = {10.15485/1865729},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Sat Jan 01 04:00:00 UTC 2022},

  month        = {Sat Jan 01 04:00:00 UTC 2022}

}

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DOI: https://doi.org/10.15485/1865729

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