POPPy — the Phyto-Ontology Platform for Pharmacology — is the first FAIR knowledge graph of medicinal-plant pharmacology: it links plants, their phytochemicals, the molecular targets those chemicals act on, and the therapeutic and clinical evidence behind them, in a form built to be read by machines as readily as by people. It is developed and maintained by the Romano Lab at the University of Pennsylvania, with input from collaborators across ethnobotany, cheminformatics, and knowledge-graph engineering.
Plants have been an essential part of medicine throughout human history. Willow bark, traditionally used to treat fever, headaches, and inflammation, was the blueprint for modern-day aspirin. Sweet wormwood was crucial in developing artemisinin, a malaria treatment that earned Tu Youyou the Nobel Prize in 2015.
Yet large-scale studies to discover new therapeutics have been hindered by an underdeveloped data infrastructure linking plant-derived compounds with known biological activities and current medicinal uses. Although there exist many medical plant databases, they are often region-specific, with disjoint features, and no standardization across sources. Other resources, like natural-product ontologies, don't distinguish between plant- and animal-derived compounds.
Through POPPy, we identify structured and unstructured sources of medicinal plants and harmonize them to include known active phytochemicals, phytochemical targets (if known), and sources and citations. This data is then mapped onto an ontology — a logic-based representation that structures concepts and their relationships into a FAIR, machine-readable knowledge graph in which every fact remains traceable to its source. POPPy itself is not a primary source, rather, it is a secondary resource that aims to guide phytotherapy research and drug discovery.
This resource was developed on Lenapehoking, the traditional ancestral homeland of the Lenape people.
"Everything on the earth has a purpose, every disease an herb to cure it."— Mourning Dove