| Bioeconomy is an industrial system with significant magnitude that relies on biological science and biotechnology,serving as a driving force in modern economics.Strains play a crucial role in achieving success in the bioeconomy,and synthetic biology is widely used to manipulate industrial microorganisms for producing various products.Currently,Escherichia coli and other model strains are often employed for industrial production.However,many non-model strains with excellent characteristics are affected by the lack of genetic tools and data.Among such strains,Zymomonas mobilis is renowned for its excellent industrial properties,such as the production of bioethanol and high-value biochemical products.Since the complete genome sequence of Z.mobilis was first reported in 2005,researchers have conducted continuous omics studies,accumulating vast amounts of omics data.Nevertheless,there exists a lack of systematic databases capable of organizing,retrieving,mining,and analyzing these multi-omics data within the domain of model strains like E.coli.This study developed and created Zym Omics(http://zymomics.cn).To build the Zym Omics database website,a one-stop visual online database website for Z.mobilis.In order to build the Zym Omics database website,the study conducted an early-stage requirements analysis to determine the four core requirements of website data display,data search,data analysis,and data visualization,as well as the non-functional requirements of the editing backend.Based on this analysis,the study adopted the idea of separating the website front-end and back-end and modular development.By using the Vue.js framework and various component libraries,the front-end development of the Zym Omics website and editing backend were successfully completed.Furthermore,Python was used to complete the server-side development.To ensure that the data results are displayed in the best possible way,Echarts and G2 were utilized to visualize the data analysis and results.To further assist researchers without programming experience,the study also provides data analysis processes for genomics,transcriptomics,and metabolic pathways.Overall,the creation of Zym Omics represents a significant advancement in the field of Z.mobilis research and will undoubtedly serve as a valuable resource for researchers worldwide.At present,Zym Omics contains genomic information for all publicly available strains of Z.mobilis.The 2001 genes,proteins and 366 multi-omics expression data have been organized based on the ZM4 strain.Furthermore,Zym Omics obtained homologous proteins of the ZM4 strain with E.coli str.K-12 MG1655 and Saccharomyces cerevisiae S288 C through blastp.The protein-protein interaction relationship of the ZM4 strain was acquired through the STRING database API.All known protein crystal structures were gathered from Uniprot.All known protein crystal structures were gathered from Uniprot,while all protein crystal structures were predicted using Alphafold2.A total of 191 biological components were collected from literature and i GEM database.Online data analysis processes were independently developed,including WGS Re-seq analysis for second-generation resequencing,Long-read analysis for third-generation resequencing,RNA-seq analysis for transcriptome sequencing,CRISPR＿TA＿RM analysis for CRISPR system and visualization of metabolic model pathway analysis Metabolic model.Additionally,Practical tool websites and real-time updated literature related to Z.mobilis are also available.Zym Omics provides a rapid search and analysis platform for researchers of non-model organism Z.mobilis.Zym Omics offers a quick search and analysis platform for researchers focused on non-model organism Z.mobilis.The unified platform can provide a reference and standard for researchers in this field to collect and process data,making it easier to conduct comparative analysis in the future.Moreover,the platform’s analysis process not only assesses data for Z.mobilis,but also provides in-depth analysis and visualization of omics data and metabolic pathways for researchers studying other microorganisms. |
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