BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
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DOI：
10.1093/nar/gkv1049
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Lewis NE
中科院分区：
文献类型：
--
作者：
King ZA;Lu J;Dräger A;Miller P;Federowicz S;Lerman JA;Ebrahim A;Palsson BO;Lewis NE
基因组规模的代谢模型是可用于预测代谢途径使用和生长表型的遗传结构知识库。此外，当与实验数据相结合时，它们可以生成和测试假设。为了最大限度地发挥这些模型的价值，必须建立高质量模型的中央储存库，模型必须遵守既定标准，模型组成部分必须与相关数据库相连接。模型可视化工具进一步增强了其实用性。为了满足这些需求，我们提出了BiGG模型（bigg.ucsd.edu），这是一个完全重新设计的生物化学，遗传学和基因组学知识库。BiGG Models包含超过75个高质量的人工基因组规模代谢模型。在网站上，用户可以浏览，搜索和可视化模型。BiGG Models将基因组规模的模型连接到基因组注释和外部数据库。反应和代谢物标识符已在模型中标准化，以符合社区标准，并能够在模型之间进行快速比较。此外，BiGG Models提供了一个全面的应用程序编程接口，用于通过建模和分析工具访问BiGG Models。作为高度策划、标准化和易于访问的代谢模型的资源，BiGG模型将促进多样化的系统生物学研究并支持对多样化实验数据进行基于知识的分析。
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.