SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
Abstract Background Reaction networks are widely used as mechanistic models in systems biology to reveal principles of biological systems. Reactions are governed by kinetic laws that describe reaction rates. Selecting the appropriate kinetic laws is difficult for many modelers. There exist tools tha...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-023-05380-3 |
| _version_ | 1797801272272748544 |
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| author | Jin Xu |
| author_facet | Jin Xu |
| author_sort | Jin Xu |
| collection | DOAJ |
| description | Abstract Background Reaction networks are widely used as mechanistic models in systems biology to reveal principles of biological systems. Reactions are governed by kinetic laws that describe reaction rates. Selecting the appropriate kinetic laws is difficult for many modelers. There exist tools that attempt to find the correct kinetic laws based on annotations. Here, I developed annotation-independent technologies that assist modelers by focusing on finding kinetic laws commonly used for similar reactions. Results Recommending kinetic laws and other analyses of reaction networks can be viewed as a classification problem. Existing approaches to determining similar reactions rely heavily on having good annotations, a condition that is often unsatisfied in model repositories such as BioModels. I developed an annotation-independent approach to find similar reactions via reaction classifications. I proposed a two-dimensional kinetics classification scheme (2DK) that analyzed reactions along the dimensions of kinetics type (K type) and reaction type (R type). I identified approximately ten mutually exclusive K types, including zeroth order, mass action, Michaelis–Menten, Hill kinetics, and others. R types were organized by the number of distinct reactants and the number of distinct products in reactions. I constructed a tool, SBMLKinetics, that inputted a collection of SBML models and then calculated reaction classifications as the probability of each 2DK class. The effectiveness of 2DK was evaluated on BioModels, and the scheme classified over 95% of the reactions. Conclusions 2DK had many applications. It provided a data-driven annotation-independent approach to recommending kinetic laws by using type common for the kind of models in combination with the R type of the reactions. Alternatively, 2DK could also be used to alert users that a kinetic law was unusual for the K type and R type. Last, 2DK provided a way to analyze groups of models to compare their kinetic laws. I applied 2DK to BioModels to compare the kinetics of signaling networks with the kinetics of metabolic networks and found significant differences in K type distributions. |
| first_indexed | 2024-03-13T04:47:56Z |
| format | Article |
| id | doaj.art-db8461b534c743d68a812c5fd3ba00f3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-13T04:47:56Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-db8461b534c743d68a812c5fd3ba00f32023-06-18T11:26:20ZengBMCBMC Bioinformatics1471-21052023-06-0124111610.1186/s12859-023-05380-3SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML modelsJin Xu0Department of Bioengineering, University of WashingtonAbstract Background Reaction networks are widely used as mechanistic models in systems biology to reveal principles of biological systems. Reactions are governed by kinetic laws that describe reaction rates. Selecting the appropriate kinetic laws is difficult for many modelers. There exist tools that attempt to find the correct kinetic laws based on annotations. Here, I developed annotation-independent technologies that assist modelers by focusing on finding kinetic laws commonly used for similar reactions. Results Recommending kinetic laws and other analyses of reaction networks can be viewed as a classification problem. Existing approaches to determining similar reactions rely heavily on having good annotations, a condition that is often unsatisfied in model repositories such as BioModels. I developed an annotation-independent approach to find similar reactions via reaction classifications. I proposed a two-dimensional kinetics classification scheme (2DK) that analyzed reactions along the dimensions of kinetics type (K type) and reaction type (R type). I identified approximately ten mutually exclusive K types, including zeroth order, mass action, Michaelis–Menten, Hill kinetics, and others. R types were organized by the number of distinct reactants and the number of distinct products in reactions. I constructed a tool, SBMLKinetics, that inputted a collection of SBML models and then calculated reaction classifications as the probability of each 2DK class. The effectiveness of 2DK was evaluated on BioModels, and the scheme classified over 95% of the reactions. Conclusions 2DK had many applications. It provided a data-driven annotation-independent approach to recommending kinetic laws by using type common for the kind of models in combination with the R type of the reactions. Alternatively, 2DK could also be used to alert users that a kinetic law was unusual for the K type and R type. Last, 2DK provided a way to analyze groups of models to compare their kinetic laws. I applied 2DK to BioModels to compare the kinetics of signaling networks with the kinetics of metabolic networks and found significant differences in K type distributions.https://doi.org/10.1186/s12859-023-05380-3Systems biologyKineticsData analysisSoftwareComputational modeling |
| spellingShingle | Jin Xu SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models BMC Bioinformatics Systems biology Kinetics Data analysis Software Computational modeling |
| title | SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models |
| title_full | SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models |
| title_fullStr | SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models |
| title_full_unstemmed | SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models |
| title_short | SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models |
| title_sort | sbmlkinetics a tool for annotation independent classification of reaction kinetics for sbml models |
| topic | Systems biology Kinetics Data analysis Software Computational modeling |
| url | https://doi.org/10.1186/s12859-023-05380-3 |
| work_keys_str_mv | AT jinxu sbmlkineticsatoolforannotationindependentclassificationofreactionkineticsforsbmlmodels |