For Metabolites module, PCMD provides diverse pages and tools, such as Search merabolites, Search structure, Search molecular weight, Metabolites-enrichment, ID conversion and Metabolites-comparison.

  By using Search merabolites, users can explore whether metabolites of interest exist in different species and obtain whether the input metabolites are supported by experiments and other databases. The collected species classification information is used to further provide enrichment results for the families in which metabolite-enriched species mainly exist, making it convenient for users to query. Moreover, users could quickly access and download metabolites that were closest and farthest from the queried metabolites in the species distribution. Additionally, structure-based search functionality is available on the "Search structure" page, offering “Input the structure” and “Draw the structure” search modes. Molecular weight searches are conducted on the "Search molecular weight" page, where users can retrieve a list of metabolites fitting their specified molecular weight and type range. These features expand the ways metabolites can be searched, with all search results accessible by clicking on the metabolite name to view its detailed information page, including abbreviation, molecular formula, molecular weight, monoisotopic mass, and the distribution and classification of the metabolite across 530 species. If users are interested in exploring the enrichment of a specific set of metabolites across different species, we provide "Metabolites-enrichment" tool for support. Users can enter or upload a set of metabolites, and the results mainly include basic information and classification of metabolites, the distribution of input metabolites across 530 species, enrichment analysis, and relevant literature. Additionally, we provide an ID conversion tool that enables users to efficiently convert metabolite IDs across 17 databases. The databases involved are Biocyc, PubChem, CHEBI, KEGG, CAS, ChEMBL, MetanetX, NIKKAJI, KNApSAcK, 3DMET, ChemSpider, SEED, PDB-CCD, HMDB, BiGG, Metabolights, PMhub. Users can perform ID conversion across different platforms by either inputting or uploading the metabolite IDs of interest. We also offer the Metabolites-comparison tool, which enables users to upload and annotate their own metabolite data and compare them with the data in PCMD to obtain basic information about metabolites and the distribution in 530 plant species.

  Notably, the predicted metabolites provided in PCMD are mainly based on the GEM model prediction, please refer to the Method for details. However, the GEM (Thiele and Palsson, 2010) method also has certain limitations. It is important to note that the quality of the input genome assembly and the accuracy of known metabolic pathways are crucial factors in ensuring the reliability of prediction results. The potential lack of specific information on unique plant species or specialized metabolic pathways in existing databases could lead to gaps in the reconstructed networks. Moreover, when it comes to predicting secondary metabolites, the GEM method may have shortcomings due to the inherent complexity and diversity of plant metabolic processes. The biosynthesis of secondary metabolites involves specific enzymes and reactions and is significantly influenced by environmental factors such as light, temperature, and pressure, which poses a challenge to the accurate simulation and prediction of GEMs. Future developments in the field should focus on addressing these challenges, potentially leading to more robust and comprehensive models capable of accurately representing the metabolic intricacies of diverse plant species.

The information of 17 databases involved in the ID conversion tool

Tutorials for each sub-module

References