#33 · Tools & infrastructure

Knowledge graphs integrate metabolite, microbial, and trait data for queryable biology

The common thread is machine-readable integration of heterogeneous biological records into structures that can be queried. METRIN-KG joins plant metabolomes, trait data, and biotic interaction records within a knowledge graph exposed through an interactive search interface. KG-Microbe provides a modular construction framework that harmonizes bacterial and archaeal data and supports customizable taxa subsets. The Daphnia magna entry addresses an upstream step: deep metabolome annotation that combines multi-platform MS and NMR data with a Galaxy pipeline of more than 30 tools, yielding 8,181 annotated metabolites. Its output is an annotated compound inventory rather than a graph, so it does not share the graph-construction method of the other two entries. What is new in this set is the pairing of graph-based integration with workflow-level metabolite annotation for a specific ecotoxicological organism.