Metazen – metadata capture for metagenomes
Abstract
Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to addmore »
- Authors:
-
- Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1224089
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; metadata; metagenomics; collection; software
Citation Formats
Bischof, Jared, Harrison, Travis, Paczian, Tobias, Glass, Elizabeth, Wilke, Andreas, and Meyer, Folker. Metazen – metadata capture for metagenomes. United States: N. p., 2014.
Web. doi:10.1186/1944-3277-9-18.
Bischof, Jared, Harrison, Travis, Paczian, Tobias, Glass, Elizabeth, Wilke, Andreas, & Meyer, Folker. Metazen – metadata capture for metagenomes. United States. https://doi.org/10.1186/1944-3277-9-18
Bischof, Jared, Harrison, Travis, Paczian, Tobias, Glass, Elizabeth, Wilke, Andreas, and Meyer, Folker. Mon .
"Metazen – metadata capture for metagenomes". United States. https://doi.org/10.1186/1944-3277-9-18. https://www.osti.gov/servlets/purl/1224089.
@article{osti_1224089,
title = {Metazen – metadata capture for metagenomes},
author = {Bischof, Jared and Harrison, Travis and Paczian, Tobias and Glass, Elizabeth and Wilke, Andreas and Meyer, Folker},
abstractNote = {Background: As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. These tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results: Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusion: Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.},
doi = {10.1186/1944-3277-9-18},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 9,
place = {United States},
year = {Mon Dec 08 00:00:00 EST 2014},
month = {Mon Dec 08 00:00:00 EST 2014}
}
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