T. Klamt, A. Jaczkowski, J. Franke, W. Nejdl
Natural products remain one of the most productive sources of pharmacologically active compounds for drug discovery. Open aggregators attribute licenses at database granularity, and the consequences of that choice have become tangible: the September 2024 transition of the Natural Products Atlas to CC BY-NC 4.0 shows how a single source's relicensing propagates across an aggregate. THEOBROMA, accessible at https://theobroma.l3s.uni-hannover.de, integrates 1,132,805 natural products from 29 open sources under a per-compound license audit that resolves each compound's license tier across all attesting sources under a most-restrictive-wins rule, identifying 900,103 compounds (79.5%) under open-use licenses and providing the per-source attestation chain and resolved tier through a dedicated audit endpoint and a query-time license filter. A three-tier classification labels all but 21 compounds by the provenance of the assignment (55.3% source-supplied labels, 18.2% NPClassifier tool assignments, 26.5% model-inferred). Deduplication at the full 27-character InChIKey retains 1,132,805 entries across 486,032 connectivity families, exposed via a dedicated /api/stereoisomers/ endpoint and a radial-family display. Per-compound license provenance is the primary differentiator. Classification stratification and stereoisomer-family exposure add finer-grained access to two related axes, supporting license-compatible virtual screening and isomer-specific bioactivity analysis at corpus scale.