Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
04 Sep 2024
04 Sep 2024
Historique:
received:
25
01
2024
accepted:
13
08
2024
medline:
5
9
2024
pubmed:
5
9
2024
entrez:
4
9
2024
Statut:
epublish
Résumé
The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. "Digital Microbes" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.
Identifiants
pubmed: 39232008
doi: 10.1038/s41597-024-03778-z
pii: 10.1038/s41597-024-03778-z
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
967Subventions
Organisme : National Science Foundation (NSF)
ID : 1746045
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : National Science Foundation (NSF)
ID : OCE-2019589
Organisme : Simons Foundation
ID : 542391
Informations de copyright
© 2024. The Author(s).
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