PlantMetWiki: a FAIR knowledge graph for plant metabolic pathway cross-species representation and integration
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.
### Competing Interest Statement
The authors declare the following financial interests and personal relationships which may be considered as potential competing interests: J.J.J.vdH. is a member of the Scientific Advisory Board of NAICONS Srl., Milano, Italy and consults for Corteva Agriscience, Indianapolis, IN, USA. M.H.M. is a member of the Scientific Advisory Boards of Hexagon Bio and Hothouse Therapeutics Ltd. All other authors declare to have no competing interests.
Netherlands Organization for Scientific Research (NWO), Vidi Grant VI.Vidi.213.183
4TU Research Data, FAIR data fund 4th edition