Improving the usability and comprehensiveness of microbial databases

Improving the usability and comprehensiveness of microbial databases

Abstract 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 acc...

Full description

Bibliographic Details
Main Authors: Caitlin Loeffler, Aaron Karlsberg, Lana S. Martin, Eleazar Eskin, David Koslicki, Serghei Mangul
Format: Article
Language:English
Published: BMC 2020-04-01
Series:BMC Biology
Online Access:http://link.springer.com/article/10.1186/s12915-020-0756-z
id doaj-d7833fd3c7fc43cda5bcbe1bcda19637
record_format Article
spelling doaj-d7833fd3c7fc43cda5bcbe1bcda196372020-11-25T02:04:51ZengBMCBMC Biology1741-70072020-04-011811610.1186/s12915-020-0756-zImproving the usability and comprehensiveness of microbial databasesCaitlin Loeffler0Aaron Karlsberg1Lana S. Martin2Eleazar Eskin3David Koslicki4Serghei Mangul5Department of Computer Science, University of California Los AngelesDepartment of Clinical Pharmacy, University of Southern California School of PharmacyDepartment of Clinical Pharmacy, University of Southern California School of PharmacyDepartment of Computer Science, University of California Los AngelesSchool of Computer Science and Engineering, The Pennsylvania State UniversityDepartment of Clinical Pharmacy, University of Southern California School of PharmacyAbstract 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.http://link.springer.com/article/10.1186/s12915-020-0756-z
collection DOAJ
language English
format Article
sources DOAJ
author Caitlin Loeffler
Aaron Karlsberg
Lana S. Martin
Eleazar Eskin
David Koslicki
Serghei Mangul
spellingShingle Caitlin Loeffler
Aaron Karlsberg
Lana S. Martin
Eleazar Eskin
David Koslicki
Serghei Mangul
Improving the usability and comprehensiveness of microbial databases
BMC Biology
author_facet Caitlin Loeffler
Aaron Karlsberg
Lana S. Martin
Eleazar Eskin
David Koslicki
Serghei Mangul
author_sort Caitlin Loeffler
title Improving the usability and comprehensiveness of microbial databases
title_short 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_sort improving the usability and comprehensiveness of microbial databases
publisher BMC
series BMC Biology
issn 1741-7007
publishDate 2020-04-01
description Abstract 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.
url http://link.springer.com/article/10.1186/s12915-020-0756-z
work_keys_str_mv AT caitlinloeffler improvingtheusabilityandcomprehensivenessofmicrobialdatabases
AT aaronkarlsberg improvingtheusabilityandcomprehensivenessofmicrobialdatabases
AT lanasmartin improvingtheusabilityandcomprehensivenessofmicrobialdatabases
AT eleazareskin improvingtheusabilityandcomprehensivenessofmicrobialdatabases
AT davidkoslicki improvingtheusabilityandcomprehensivenessofmicrobialdatabases
AT sergheimangul improvingtheusabilityandcomprehensivenessofmicrobialdatabases
_version_ 1724940696548278272

Similar Items