Improving the usability and comprehensiveness of microbial databases

Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibilit...

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Autores principales: Loeffler, Caitlin, Karlsberg, Aaron, Martin, Lana S., Eskin, Eleazar, Koslicki, David, Mangul, Serghei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Comment
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140547/
https://www.ncbi.nlm.nih.gov/pubmed/32264902
http://dx.doi.org/10.1186/s12915-020-0756-z
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author Loeffler, Caitlin
Karlsberg, Aaron
Martin, Lana S.
Eskin, Eleazar
Koslicki, David
Mangul, Serghei
author_facet Loeffler, Caitlin
Karlsberg, Aaron
Martin, Lana S.
Eskin, Eleazar
Koslicki, David
Mangul, Serghei
author_sort Loeffler, Caitlin
collection PubMed
description Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research.
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spelling pubmed-71405472020-04-14 Improving the usability and comprehensiveness of microbial databases Loeffler, Caitlin Karlsberg, Aaron Martin, Lana S. Eskin, Eleazar Koslicki, David Mangul, Serghei BMC Biol Comment Metagenomics studies leverage genomic reference databases to generate discoveries in basic science and translational research. However, current microbial studies use disparate reference databases that lack consistent standards of specimen inclusion, data preparation, taxon labelling and accessibility, hindering their quality and comprehensiveness, and calling for the establishment of recommendations for reference genome database assembly. Here, we analyze existing fungal and bacterial databases and discuss guidelines for the development of a master reference database that promises to improve the quality and quantity of omics research. BioMed Central 2020-04-07 /pmc/articles/PMC7140547/ /pubmed/32264902 http://dx.doi.org/10.1186/s12915-020-0756-z Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Comment
Loeffler, Caitlin
Karlsberg, Aaron
Martin, Lana S.
Eskin, Eleazar
Koslicki, David
Mangul, Serghei
Improving the usability and comprehensiveness of microbial databases
title Improving the usability and comprehensiveness of microbial databases
title_full Improving the usability and comprehensiveness of microbial databases
title_fullStr Improving the usability and comprehensiveness of microbial databases
title_full_unstemmed Improving the usability and comprehensiveness of microbial databases
title_short Improving the usability and comprehensiveness of microbial databases
title_sort improving the usability and comprehensiveness of microbial databases
topic Comment
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140547/
https://www.ncbi.nlm.nih.gov/pubmed/32264902
http://dx.doi.org/10.1186/s12915-020-0756-z
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