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MediaDive: the expert-curated cultivation media database

We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designe...

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Detalles Bibliográficos
Autores principales: Koblitz, Julia, Halama, Philipp, Spring, Stefan, Thiel, Vera, Baschien, Christiane, Hahnke, Richard L, Pester, Michael, Overmann, Jörg, Reimer, Lorenz Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825534/
https://www.ncbi.nlm.nih.gov/pubmed/36134710
http://dx.doi.org/10.1093/nar/gkac803
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author Koblitz, Julia
Halama, Philipp
Spring, Stefan
Thiel, Vera
Baschien, Christiane
Hahnke, Richard L
Pester, Michael
Overmann, Jörg
Reimer, Lorenz Christian
author_facet Koblitz, Julia
Halama, Philipp
Spring, Stefan
Thiel, Vera
Baschien, Christiane
Hahnke, Richard L
Pester, Michael
Overmann, Jörg
Reimer, Lorenz Christian
author_sort Koblitz, Julia
collection PubMed
description We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms.
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spelling pubmed-98255342023-01-10 MediaDive: the expert-curated cultivation media database Koblitz, Julia Halama, Philipp Spring, Stefan Thiel, Vera Baschien, Christiane Hahnke, Richard L Pester, Michael Overmann, Jörg Reimer, Lorenz Christian Nucleic Acids Res Database Issue We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instructions and molecular compositions of >3200 standardized cultivation media for >40 000 microbial strains from all domains of life. MediaDive is designed to enable broad range applications from every-day-use in research and diagnostic laboratories to knowledge-driven support of new media design and artificial intelligence-driven data mining. It offers a number of intuitive search functions and comparison tools, for example to identify media for related taxonomic groups and to integrate strain-specific modifications. Besides classical PDF archiving and printing, the state-of-the-art website allows paperless use of media recipes on mobile devices for convenient wet-lab use. In addition, data can be retrieved using a RESTful web service for large-scale data analyses. An internal editor interface ensures continuous extension and curation of media by cultivation experts from the Leibniz Institute DSMZ, which is interlinked with the growing microbial collections at DSMZ. External user engagement is covered by a dedicated media builder tool. The standardized and programmatically accessible data will foster new approaches for the design of cultivation media to target the vast majority of uncultured microorganisms. Oxford University Press 2022-09-22 /pmc/articles/PMC9825534/ /pubmed/36134710 http://dx.doi.org/10.1093/nar/gkac803 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Koblitz, Julia
Halama, Philipp
Spring, Stefan
Thiel, Vera
Baschien, Christiane
Hahnke, Richard L
Pester, Michael
Overmann, Jörg
Reimer, Lorenz Christian
MediaDive: the expert-curated cultivation media database
title MediaDive: the expert-curated cultivation media database
title_full MediaDive: the expert-curated cultivation media database
title_fullStr MediaDive: the expert-curated cultivation media database
title_full_unstemmed MediaDive: the expert-curated cultivation media database
title_short MediaDive: the expert-curated cultivation media database
title_sort mediadive: the expert-curated cultivation media database
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825534/
https://www.ncbi.nlm.nih.gov/pubmed/36134710
http://dx.doi.org/10.1093/nar/gkac803
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