THEOBROMA v1.35: an open multi-kingdom natural-products database

THEOBROMA is an aggregated open natural-products database containing 1,132,805compounds from 29 source databases across four biological kingdoms plus anunresolved category. The corpus preserves full 27-character InChIKeys and exposesthe resulting 486,032 stereoisomer families as a directly queryable resource.Provenance is tracked at compound granularity for both classification (source-inherited, NPClassifier tool, or model-inferred) and licensing (per-compoundresolution across all attesting sources under a most-restrictive-wins rule, witha least-restrictive bound reported alongside it). Open-licensed compound coverage is 79.5% of the corpus under the most restrictiveresolution and 91.2% under the least restrictive. License tiers are recorded percompound in the license_tier and tier_rank_min columns for downstream filtering:891,860 compounds resolve to CC BY 4.0, 8,243 to CC0, 225,536 to CC BY-NC 4.0,and 7,166 to sources with unspecified terms. The deposit comprises a PostgreSQL custom-format archive of 18 relational tables(compounds, compound_taxonomy, resolved_taxonomy, per_source_license_attestation,source_license_ref, compound_synonyms, compound_region_map, admet, scaffolds, theNPClassifier ontology tables, and the taxonomy reference tables), the classifierreproducibility bundle (XGBoost model, PCA basis, Optuna study, per-classevaluation, threshold calibration), and the per-source reproducibility manifest.Restore requires the pg_trgm extension for the trigram name index. This record declares three licenses because the corpus is not uniformly licensed.CC BY 4.0 covers the contributed layer: the license audit and resolved tiers, theclassification, the taxonomy resolution, and the schema. CC BY-NC 4.0 and CC0 1.0are declared because upstream source terms flow through unchanged at compoundgranularity. Downstream use should be governed by the license_tier column ratherthan by any single record-level designation. The accompanying live database is at https://theobroma.l3s.uni-hannover.de andsource code at https://github.com/ThorKlm/theobroma. This deposit accompanies thepreprint at https://doi.org/10.64898/2026.06.12.731585.