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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, cont...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145653/ https://www.ncbi.nlm.nih.gov/pubmed/31696234 http://dx.doi.org/10.1093/nar/gkz1054 |
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author | Norsigian, Charles J Pusarla, Neha McConn, John Luke Yurkovich, James T Dräger, Andreas Palsson, Bernhard O King, Zachary |
author_facet | Norsigian, Charles J Pusarla, Neha McConn, John Luke Yurkovich, James T Dräger, Andreas Palsson, Bernhard O King, Zachary |
author_sort | Norsigian, Charles J |
collection | PubMed |
description | The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models. |
format | Online Article Text |
id | pubmed-7145653 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71456532020-04-13 BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree Norsigian, Charles J Pusarla, Neha McConn, John Luke Yurkovich, James T Dräger, Andreas Palsson, Bernhard O King, Zachary Nucleic Acids Res Database Issue The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models. Oxford University Press 2020-01-08 2019-11-07 /pmc/articles/PMC7145653/ /pubmed/31696234 http://dx.doi.org/10.1093/nar/gkz1054 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://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 Norsigian, Charles J Pusarla, Neha McConn, John Luke Yurkovich, James T Dräger, Andreas Palsson, Bernhard O King, Zachary BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title | BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title_full | BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title_fullStr | BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title_full_unstemmed | BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title_short | BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
title_sort | bigg models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145653/ https://www.ncbi.nlm.nih.gov/pubmed/31696234 http://dx.doi.org/10.1093/nar/gkz1054 |
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