In the past, microbial strain data were scattered across the literature and internal files of culture collections. Here we describe the current development of a new infrastructure of databases to advance science by providing standardised microbial strain information through state-of-the-art websites. The DSMZ services BacDive, StrainInfo, MediaDive and LPSN provide up-to-date knowledge on various aspects of microbial strains. BacDive is the largest knowledgebase of standardised prokaryotic strain data and uses AI techniques to predict traits and to fill the gaps for less well studied species, which also has the potential to increase knowledge about the majority of uncultured microorganisms. The aim of the newly implemented StrainInfo database is to serve as a one-stop-shop for strain identity information, culture details from repositories, associated sequences and literature. A future extension will include a strain registry for type cultures of new microbial species. The MediaDive database provides a comprehensive, expert-curated database of culture media to help find a medium for a wide range of microorganisms, with future AI-based predictions of new media based on genomic and metabolic properties. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is the nomenclature repository for prokaryotes, providing up-to-date nomenclatural data including type strain information.
For the future of microbial strain data, a new exchange standard is envisioned. A new open standard, that is followed by several microbial databases and culture collections, will enable barrier-free data flow between different systems, ultimately overcoming the problem of dependency on single services.
Reimer L.C., Schober I., Lissin A., Sardà Carbasse J., Witte J.F., Koblitz J., Yurkov A., Freese H.M., Göker M. and Overmann J. The Past, the Presence and the Future of Microbial Strain Data. IMC12, Maastricht, The Netherlands. 13.08.2024. (Invited lecture: short)
@misc{Reimer2024,
Title = {The Past, the Presence and the Future of Microbial Strain Data},
Author = {Reimer, Lorenz Christian and Schober, Isabel and Lissin, Artur and Sardà Carbasse, Joaquim and Witte, Julius F. and Koblitz, Julia and Yurkov, Andrey and Freese, Heike M. and Göker, Markus and Overmann, Jörg},
Editor = {},
Year = {2024},
Abstract = {In the past, microbial strain data were scattered across the literature and internal files of culture collections. Here we describe the current development of a new infrastructure of databases to advance science by providing standardised microbial strain information through state-of-the-art websites. The DSMZ services BacDive, StrainInfo, MediaDive and LPSN provide up-to-date knowledge on various aspects of microbial strains. BacDive is the largest knowledgebase of standardised prokaryotic strain data and uses AI techniques to predict traits and to fill the gaps for less well studied species, which also has the potential to increase knowledge about the majority of uncultured microorganisms. The aim of the newly implemented StrainInfo database is to serve as a one-stop-shop for strain identity information, culture details from repositories, associated sequences and literature. A future extension will include a strain registry for type cultures of new microbial species. The MediaDive database provides a comprehensive, expert-curated database of culture media to help find a medium for a wide range of microorganisms, with future AI-based predictions of new media based on genomic and metabolic properties. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is the nomenclature repository for prokaryotes, providing up-to-date nomenclatural data including type strain information.
For the future of microbial strain data, a new exchange standard is envisioned. A new open standard, that is followed by several microbial databases and culture collections, will enable barrier-free data flow between different systems, ultimately overcoming the problem of dependency on single services.},
}
TY - SLIDE
AU - Reimer, Lorenz Christian
AU - Schober, Isabel
AU - Lissin, Artur
AU - Sardà Carbasse, Joaquim
AU - Witte, Julius F.
AU - Koblitz, Julia
AU - Yurkov, Andrey
AU - Freese, Heike M.
AU - Göker, Markus
AU - Overmann, Jörg
TI - The Past, the Presence and the Future of Microbial Strain Data
PY - 2024
AB - In the past, microbial strain data were scattered across the literature and internal files of culture collections. Here we describe the current development of a new infrastructure of databases to advance science by providing standardised microbial strain information through state-of-the-art websites. The DSMZ services BacDive, StrainInfo, MediaDive and LPSN provide up-to-date knowledge on various aspects of microbial strains. BacDive is the largest knowledgebase of standardised prokaryotic strain data and uses AI techniques to predict traits and to fill the gaps for less well studied species, which also has the potential to increase knowledge about the majority of uncultured microorganisms. The aim of the newly implemented StrainInfo database is to serve as a one-stop-shop for strain identity information, culture details from repositories, associated sequences and literature. A future extension will include a strain registry for type cultures of new microbial species. The MediaDive database provides a comprehensive, expert-curated database of culture media to help find a medium for a wide range of microorganisms, with future AI-based predictions of new media based on genomic and metabolic properties. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is the nomenclature repository for prokaryotes, providing up-to-date nomenclatural data including type strain information.
For the future of microbial strain data, a new exchange standard is envisioned. A new open standard, that is followed by several microbial databases and culture collections, will enable barrier-free data flow between different systems, ultimately overcoming the problem of dependency on single services.
CY - Maastricht, The Netherlands
ER -
