AI Insight
PlantMetWiki is a new knowledge graph database that integrates plant metabolic pathway information across multiple species using FAIR (Findable, Accessible, Interoperable, Reusable) principles and Linked Open Data standards. The resource contains 1,162 plant metabolic pathways converted from PlantCyc 17.0 into RDF format, with cross-links to biosynthetic gene clusters, metabolite databases, and genomic context information. It enables researchers to perform comparative analyses across plant species, identify knowledge gaps, and integrate metabolic pathway data with external chemical databases through federated queries.
Why it matters
This resource addresses a major bottleneck in plant natural product discovery by consolidating fragmented pathway information scattered across different databases and publications. By enabling systematic cross-species comparisons and integration with multi-omics data, PlantMetWiki could accelerate the discovery of novel plant compounds with potential applications in pharmaceuticals, agriculture, and industrial biotechnology.
Understand the Science
⚠️ Preprint – Noch nicht peer-reviewed
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Plants produce a vast diversity of specialized metabolites with extensive potential ecological, agro-industrial, and pharmaceutical applications. Discovery of novel plant natural products relies on combining multi-omics evidence with biochemical transformations. However, pathway-level annotations are fragmented across individual species, databases, and publications, limiting comparative cross-species pathway analyses and systematic generation of hypotheses. To support integration and reuse of plant metabolic knowledge, we developed PlantMetWiki, a FAIR Linked Open Data semantically enriched knowledge graph built on infrastructure adapted from WikiPathways. Our approach extends on the highly curated pathway information from Plant Metabolic Network with crosslinks to biosynthetic gene clusters resources (MIBiG and plantiSMASH), metabolite annotations, and cross-species modelling. This way, our resource captures pathway genomic context, increases metabolomics data interoperability via federated queries, and supports cross-species analysis to identify annotation gaps. PlantMetWiki represents 1,162 plant metabolic pathways as Resource Description Framework (RDF) graphs, preserving pathway structure, literature provenance, annotations, and taxonomic information from PlantCyc 17.0. PlantMetWiki is distributed through a public SPARQL endpoint with open-source reproducible data transformation and validation workflows. By modelling pathways as a multispecies graph, PlantMetWiki enables comparative analyses across taxa, integration with external chemical knowledge resources through federated queries, and identification of metabolic, genomic, and chemical annotation gaps. As a result, PlantMetWiki provides a foundation for FAIR reuse and integration of plant pathway knowledge.