The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
| Autor: | Qizhi Zhang, Nicholas Chia, Michael B. Mundy, Patrik D'haeseleer, Christopher S. Henry, Aaron A. Best, Erik Pearson, Matthew DeJongh, Shane Canon, Janaka N. Edirisinghe, Filipe Liu, Robert W. Cottingham, Jeffrey A. Kimbrel, Moritz Emanuel Beber, José P. Faria, Elad Noor, Sean R. McCorkle, Samuel M. D. Seaver, Elisha M. Wood-Charlson, James G. Jeffryes, Adam P. Arkin, Jay R. Bolton |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Databases Factual AcademicSubjects/SCI00010 Biology computer.software_genre 01 natural sciences Biochemical network Set (abstract data type) 03 medical and health sciences Databases Resource (project management) 0302 clinical medicine Information and Computing Sciences Genetics Database Issue Factual 030304 developmental biology 2. Zero hunger 0303 health sciences Genome Database Bacteria Bacterial Fungi Chemical data Molecular Sequence Annotation Biological Sciences Plants Plant genomes Flux balance analysis Metabolic pathway Networking and Information Technology R&D Biochemistry Nucleic acid Thermodynamics Corrigendum computer 030217 neurology & neurosurgery Environmental Sciences Genome Bacterial Metabolic Networks and Pathways 010606 plant biology & botany Developmental Biology |
| Zdroj: | Nucleic Acids Research Nucleic acids research, vol 49, iss D1 Seaver, S M D, Liu, F, Zhang, Q, Jeffryes, J, Faria, J P, Edirisinghe, J N, Mundy, M, Chia, N, Noor, E, Beber, M E, Best, A A, DeJongh, M, Kimbrel, J A, D'haeseleer, P, McCorkle, S R, Bolton, J R, Pearson, E, Canon, S, Wood-Charlson, E M, Cottingham, R W, Arkin, A P & Henry, C S 2021, ' The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes ', Nucleic Acids Research, vol. 49, no. D1, pp. D575–D588 . https://doi.org/10.1093/nar/gkaa746 Nucleic Acids Research, 49 (D1) |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkaa746 |
| Popis: | For over 10 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/biochem and KBase. |
| Databáze: | OpenAIRE |
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