THEOBROMA 发布含 113 万天然产物的开放数据库，按化合物审计许可
THEOBROMA: an aggregated open database of 1.13 million natural products with per-compound license auditing, three-tier classification, and stereochemistry-aware deduplication
THEOBROMA 发布了一个整合 29 个开放来源、共 1 132 805 个天然产物的开放数据库，并对每个化合物逐一进行许可审计。数据库按最严格许可优先的规则，解析每个化合物在所有来源中的许可层级，其中 896 242 个化合物（79.12%）属于开放使用许可；来源证明链和解析后的层级可通过专门的审计接口和查询时许可过滤器查看。数据库还提供三层分类，除 21 个化合物外均标注了来源：55.3% 来自人工整理来源标签，18.2% 来自 NPClassifier 工具分配，26.5% 为模型推断。
来源：Nucleic Acids Research · doi.org
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 as the field grows. A recent relicensing event in one constituent source (the September 2024 transition of the Natural Products Atlas to CC BY-NC 4.0) demonstrates how database-level licensing propagates across an aggregate and motivates the per-compound audit framework presented here. The same peer cohort separately leaves classification provenance and stereoisomer-family relations coarser than either layer warrants. 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. 896 242 compounds (79.12%) are identified under open-use licenses, and the per-source attestation chain, together with the resolved tier, is exposed 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% curated source 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/<comp_id> endpoint and a radial-family display. Any result set renders directly onto a taxonomic cladogram of its source organisms, so compositional queries are answered in the interface rather than downstream. Per-compound license provenance is the primary differentiator, while classification stratification and stereoisomer-family exposure add finer-grained access to two related axes. Together, they support license-compatible virtual screening and isomer-specific bioactivity analysis at corpus scale. As an evolving open resource, THEOBROMA pairs continuous pipeline maintenance with interactive geographic, taxonomic, and chemical-space exploration.