Ontologies for Natural Product Therapeutics: Standardizing Phytochemicals, Biological Activities, Targets, Pathways, Formulations, and Evidence Levels

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Natural product therapeutics are represented across heterogeneous chemical, biological, ethnopharmacological, pharmacological, and safety data sources, yet their interpretation often depends on inconsistent terminology, incomplete provenance, weakly defined relationships, and unclear evidence boundaries. This article proposes a conceptual ontology structure for natural product therapeutics that standardizes phytochemical entities, chemical classes, compound identifiers, synonyms, stereochemistry, natural product sources, botanical context, preparation methods, extraction context, formulation entities, biological activities, assay settings, targets, pathways, disease or phenotype contexts, safety evidence, traditional use evidence, and evidence levels. The proposed framework distinguishes controlled vocabularies, taxonomies, ontologies, knowledge graphs, database schemas, semantic classes, entity attributes, semantic relationships, provenance fields, uncertainty fields, and claim-support boundaries. It emphasizes that ontology-based standardization can improve semantic consistency, interoperability, evidence tracing, query logic, and computational reasoning, but cannot by itself validate mechanisms, efficacy, safety, therapeutic equivalence, or regulatory claims. The ontology approach links phytochemical identity to source and preparation context, connects bioactivity to assay provenance, separates target and pathway annotation from causal interpretation, and places formulation and evidence entities within explicit decision-boundary logic. The contribution is a cautious original ontology model intended to support transparent evidence organization and responsible interpretation in natural product therapeutic research.