Metadag: a web tool to generate and analyse metabolic networks
Abstract Background MetaDAG is a web-based tool developed to address challenges posed by big data from omics technologies, particularly in metabolic network reconstruction and analysis. The tool is capable of constructing metabolic networks for specific organisms, sets of organisms, reactions, enzym...
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| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06048-w |
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| author | Pere Palmer-Rodríguez Ricardo Alberich Mariana Reyes-Prieto José A. Castro Mercè Llabrés |
| author_facet | Pere Palmer-Rodríguez Ricardo Alberich Mariana Reyes-Prieto José A. Castro Mercè Llabrés |
| author_sort | Pere Palmer-Rodríguez |
| collection | DOAJ |
| description | Abstract Background MetaDAG is a web-based tool developed to address challenges posed by big data from omics technologies, particularly in metabolic network reconstruction and analysis. The tool is capable of constructing metabolic networks for specific organisms, sets of organisms, reactions, enzymes, or KEGG Orthology (KO) identifiers. By retrieving data from the KEGG database, MetaDAG helps users visualize and analyze complex metabolic interactions efficiently. Results MetaDAG computes two models: a reaction graph and a metabolic directed acyclic graph (m-DAG). The reaction graph represents reactions as nodes and metabolite flow between them as edges. The m-DAG simplifies the reaction graph by collapsing strongly connected components, significantly reducing the number of nodes while maintaining connectivity. MetaDAG can generate metabolic networks from various inputs, including KEGG organisms or custom data (e.g., reactions, enzymes, KOs). The tool displays these models on an interactive web page and provides downloadable files, including network visualizations. MetaDAG was tested using two datasets. In an eukaryotic analysis, it successfully classified organisms from the KEGG database at the kingdom and phylum levels. In a microbiome study, MetaDAG accurately distinguished between Western and Korean diets and categorized individuals by weight loss outcomes based on dietary interventions. Conclusion MetaDAG offers an effective and versatile solution for metabolic network reconstruction from diverse data sources, enabling large-scale biological comparisons. Its ability to generate synthetic metabolisms and its broad application, from taxonomy classification to diet analysis, make it a valuable tool for biological research. MetaDAG is available online, with user support provided via a comprehensive guide. MetaDAG: https://bioinfo.uib.es/metadag/ User guide: https://biocom-uib.github.io/MetaDag/ |
| format | Article |
| id | doaj-art-1886f9996f41484aaf4cef1059f9607c |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-1886f9996f41484aaf4cef1059f9607c2025-02-02T12:44:59ZengBMCBMC Bioinformatics1471-21052025-01-0126112110.1186/s12859-025-06048-wMetadag: a web tool to generate and analyse metabolic networksPere Palmer-Rodríguez0Ricardo Alberich1Mariana Reyes-Prieto2José A. Castro3Mercè Llabrés4Mathematics and Computer Science Department, University of the Balearic IslandsMathematics and Computer Science Department, University of the Balearic IslandsSequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO)Biology Department, University of the Balearic IslandsMathematics and Computer Science Department, University of the Balearic IslandsAbstract Background MetaDAG is a web-based tool developed to address challenges posed by big data from omics technologies, particularly in metabolic network reconstruction and analysis. The tool is capable of constructing metabolic networks for specific organisms, sets of organisms, reactions, enzymes, or KEGG Orthology (KO) identifiers. By retrieving data from the KEGG database, MetaDAG helps users visualize and analyze complex metabolic interactions efficiently. Results MetaDAG computes two models: a reaction graph and a metabolic directed acyclic graph (m-DAG). The reaction graph represents reactions as nodes and metabolite flow between them as edges. The m-DAG simplifies the reaction graph by collapsing strongly connected components, significantly reducing the number of nodes while maintaining connectivity. MetaDAG can generate metabolic networks from various inputs, including KEGG organisms or custom data (e.g., reactions, enzymes, KOs). The tool displays these models on an interactive web page and provides downloadable files, including network visualizations. MetaDAG was tested using two datasets. In an eukaryotic analysis, it successfully classified organisms from the KEGG database at the kingdom and phylum levels. In a microbiome study, MetaDAG accurately distinguished between Western and Korean diets and categorized individuals by weight loss outcomes based on dietary interventions. Conclusion MetaDAG offers an effective and versatile solution for metabolic network reconstruction from diverse data sources, enabling large-scale biological comparisons. Its ability to generate synthetic metabolisms and its broad application, from taxonomy classification to diet analysis, make it a valuable tool for biological research. MetaDAG is available online, with user support provided via a comprehensive guide. MetaDAG: https://bioinfo.uib.es/metadag/ User guide: https://biocom-uib.github.io/MetaDag/https://doi.org/10.1186/s12859-025-06048-wMetabolic networks constructionAnalysis of metabolic networksComparison of metabolic networks |
| spellingShingle | Pere Palmer-Rodríguez Ricardo Alberich Mariana Reyes-Prieto José A. Castro Mercè Llabrés Metadag: a web tool to generate and analyse metabolic networks BMC Bioinformatics Metabolic networks construction Analysis of metabolic networks Comparison of metabolic networks |
| title | Metadag: a web tool to generate and analyse metabolic networks |
| title_full | Metadag: a web tool to generate and analyse metabolic networks |
| title_fullStr | Metadag: a web tool to generate and analyse metabolic networks |
| title_full_unstemmed | Metadag: a web tool to generate and analyse metabolic networks |
| title_short | Metadag: a web tool to generate and analyse metabolic networks |
| title_sort | metadag a web tool to generate and analyse metabolic networks |
| topic | Metabolic networks construction Analysis of metabolic networks Comparison of metabolic networks |
| url | https://doi.org/10.1186/s12859-025-06048-w |
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