For over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions;; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies, and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

中文翻译：

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ModelSEED数据库，用于集成代谢注释以及植物，真菌和微生物的代谢模型的重建，比较和分析

十多年来，ModelSEED一直是基于带注释的微生物或植物基因组构建基因组规模代谢模型草案的主要资源。生物化学数据库现已发布，是ModelSEED和KBase背后的生物化学数据的基础。生物化学数据库体现了几种特性，这些特性通过以下方式共同使其与其他已出版的生物化学资源区分开来：（i）包括分隔，转运反应，带电分子和质子对反应的平衡；（ii）由用户社区扩展，所有数据存储在GitHub中；（iii）设计为生化“罗塞塔石”，以促进对来自许多不同工具和数据库的注释进行比较和集成。该数据库是通过组合来自多种资源的化学数据而构建的，应用标准转换，识别冗余并计算热力学性质。使用通量平衡分析对ModelSEED生物化学进行连续测试，以确保生物化学网络可进行建模，并能够模拟各种表型。可以将本体设计为有助于比较和协调新陈代谢重构，这些新陈代谢重构在表示各种新陈代谢途径方面的方式有所不同。ModelSEED现在包括33,978种化合物和36,645个反应，可以在GitHub上以一组可扩展文件的形式获得，并且可以在https://modelseed.org和KBase上进行搜索。可以将本体设计为有助于比较和协调新陈代谢重构，这些新陈代谢重构在表示各种新陈代谢途径方面的方式有所不同。ModelSEED现在包括33,978种化合物和36,645种反应，可以在GitHub上以一组可扩展文件的形式获得，并且可以在https://modelseed.org和KBase上进行搜索。可以将本体设计为有助于比较和协调新陈代谢重构，这些新陈代谢重构在表示各种新陈代谢途径方面的方式有所不同。ModelSEED现在包括33,978种化合物和36,645种反应，可以在GitHub上以一组可扩展文件的形式获得，并且可以在https://modelseed.org和KBase上进行搜索。