The LOTUS Initiative for Open Natural Products Research: biological and chemical trees

Hierarchical JSON biological and chemical trees made from the LOTUS Initiative (https://doi.org/10.7554/eLife.70780) data from https://www.wikidata.org. (see 10.5281/zenodo.5794106). Formatted for PubChem Classification. File Description {date_str}_lotus_biological_tree.json Biological taxonomy tree: taxa (under Biota) with their associated natural products, structural descriptors (InChIKey, SMILES, SMARTS, CXSMILES), and literature references (DOI, PMID). {date_str}_lotus_chemical_tree.json Chemical classification tree: compounds classified using NPClassifier pathway → superclass → class hierarchy. Recommended for chemical browsing. {date_str}_lotus_chemical_tree_wikidata.json Wikidata-based chemical tree: compounds classified via P279 (subclass of) under chemical compound. Currently sparse for natural products. lotus_pubchem_tree.py Generator script (marimo notebook): reproduces all tree files from live Wikidata. Run with: uv run lotus_pubchem_tree.py export -o ./output -v