PlantMetWiki

PlantMetWiki integrates and reuses plant metabolic knowledge as a FAIR Linked Open Data semantically enriched knowledge graph for cross-species pathway representation, comparative analysis, and identification of annotation gaps.

Key Features:

• Knowledge Graph Representation: 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.
• Cross-Species Modelling: The resource models pathways as a multispecies graph to enable comparative analyses across taxa and systematic generation of hypotheses.
• Crosslinks to Biosynthetic Gene Cluster Resources: PlantMetWiki extends curated pathway information with crosslinks to MIBiG and plantiSMASH biosynthetic gene cluster resources.
• Federated Query Support: The knowledge graph increases metabolomics data interoperability via federated queries and integration with external chemical knowledge resources.
• Public SPARQL Endpoint: PlantMetWiki is distributed through a public SPARQL endpoint with open-source reproducible data transformation and validation workflows.
• Pre-written SPARQL Queries: Pre-written SPARQL queries are available for users to execute or adapt to retrieve pathway information.

Scientific Applications:

• Comparative Cross-Species Pathway Analysis: PlantMetWiki supports cross-species analysis to identify annotation gaps and enable hypothesis generation across plant taxa.
• Metabolomics Data Integration: The resource increases metabolomics data interoperability through federated queries with external resources.
• Metabolic Annotation Gap Identification: PlantMetWiki identifies metabolic, genomic, and chemical annotation gaps through multispecies graph modelling.
• Plant Natural Product Discovery: The knowledge graph supports discovery of novel plant natural products by combining multi-omics evidence with biochemical transformations.

Methodology:

PlantMetWiki is built on infrastructure adapted from WikiPathways and extends highly curated pathway information from Plant Metabolic Network with crosslinks to biosynthetic gene clusters resources, metabolite annotations, and cross-species modelling. Data transformation and validation workflows are open-source and reproducible.