The LOTUS Initiative
Published April 13, 2026 | Version v9
Dataset Open

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

Authors/Creators

  • 1. ROR icon Institute for Molecular Systems Biology
  • 2. ROR icon Collaborative Drug Discovery (United States)
  • 3. University of Fribourg

Description

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

Files

20260413_lotus_biological_tree.json

Files (781.5 MB)

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Additional details

Related works

Is derived from
Dataset: 10.5281/zenodo.5794106 (DOI)
Is described by
Journal article: 10.7554/eLife.70780 (DOI)
Is new version of
Dataset: 10.5281/zenodo.7534070 (DOI)

Funding

Swiss National Science Foundation
MetaboLinkAI 10002786