Published April 13, 2026
| Version v11
Dataset
Open
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
Authors/Creators
-
1.
Institute for Molecular Systems Biology
-
2.
Collaborative Drug Discovery (United States)
-
3.
University of Fribourg
Contributors
- 1. Friedrich-Schiller-University Jena
- 2. Institute of Organic Chemistry and Biochemistry of the CAS
- 3. University of Virginia
- 4. Maastricht University
- 5. Université de Genève
- 6. University of Illinois at Chicago
- 7. Ontario Institute for Cancer Research
- 8. University of Glasgow
Description
Tabular CSV exports of the LOTUS Initiative (https://doi.org/10.7554/eLife.70780) data from https://www.wikidata.org.
| File | Description |
|---|---|
{date_str}_frozen.csv.gz |
Core triplet table: each row is a unique (structure InChIKey, organism Wikidata QID, reference Wikidata QID) triple with organism name, reference DOI, and manual validation status. |
{date_str}_frozen_metadata.csv.gz |
Comprehensive metadata table: enriched with structural descriptors (InChI, SMILES, molecular formula, exact mass, stereocenters), chemical classifications (NPClassifier, ClassyFire), biological taxonomy (Open Tree of Life), PubChem compound properties, and literature references (DOI, PMID, PMCID). |
{date_str}_changes_report.txt |
Change report: summary of additions and removals compared to the previous version. |
lotus_exporter.py |
Generator script (marimo notebook): reproduces all output files from live Wikidata. Run with: uv run lotus_exporter.py export -o ./output -v |
Files
260413_changes_report.txt
Additional details
Related works
- Is described by
- Journal article: 10.7554/eLife.70780 (DOI)
- Is new version of
- Dataset: 10.5281/zenodo.7534071 (DOI)
Funding
- Swiss National Science Foundation
- MetaboLinkAI 10002786