lotus_natural_products — LOTUS natural products and the organisms they occur in (2021-2026)

Description

Bipartite networks of natural products (chemical structures) and the organisms in which they were found, from LOTUS, an open resource of structure-organism pairs documented in the literature, compiled from about 40 natural-product databases, curated, and shared through Wikidata, where the community can edit and extend it. Each structure-organism pair is supported by a reference (an article or book).

2021_12_20 ... 2026_04_13: the exports of the LOTUS data from Wikidata (the "frozen" datasets), one network per export: 2021-12-20, 2022-02-08, 2022-02-26, 2022-03-18, 2022-05-25, 2022-07-01, 2022-09-16, 2023-01-06 and 2026-04-13. Nodes are structures (Wikidata items with an InChIKey) and organisms (Wikidata taxa), and there is an edge between a structure and an organism for each reference that documents that the structure is found in (or produced by) the organism, so that a pair can be connected by several edges. Structures and organisms are identified by their Wikidata items. The exports have a row for each combination of the values of the properties that have several values (e.g. an organism with two GBIF identifiers); the edges are the distinct (structure, organism, reference) triples, and the several values of a property are joined with |.
processed_2021_05_28, processed_2021_12_20, processed_2022_03_23, processed_2022_05_25, processed_2022_07_01, processed_2022_09_16, processed_2023_01_13: the curated structure-organism pairs of the processing pipeline of LOTUS (the datasets from which the data of Wikidata were built), all the versions of the dataset on Zenodo, named by their publication dates (the last one, published with the same date as the previous one, by its creation date), where each edge is a documented pair as given by one of the source databases, so that a pair documented by several databases or references is connected by several edges. Nodes are structures (identified by their InChIKey) and organisms (by their cleaned name).

The networks have the following properties (structure properties are empty for organisms, and vice versa; not all of them are in every export):

(Node) is_structure: whether the node is a chemical structure (otherwise it is an organism).
(Node) wikidata (exports): the Wikidata item of the structure or organism.
(Node) name: the traditional name of the structure (its InChIKey if it has none, and in the export of 2021-12-20, which has no names of structures), or the name of the organism.
(Node) structure_inchikey, structure_inchi, structure_smiles, structure_smiles_2d, structure_molecular_formula: the identifiers and formula of the structure (InChIKey, InChI, isomeric SMILES, SMILES without stereochemistry; no formula in processed_2021_05_28).
(Node) structure_inchikey_2d, structure_inchi_2d (processed_*): the InChIKey and InChI of the structure without stereochemistry.
(Node) structure_exact_mass, structure_xlogp: the exact mass and the computed partition coefficient of the structure (NaN if not given).
(Node) structure_cid: the PubChem compound identifier of the structure (not in the processed datasets before processed_2023_01_13).
(Node) structure_name_iupac: the IUPAC name of the structure.
(Node) structure_stereocenters_total, structure_stereocenters_unspecified: the numbers of stereocenters of the structure, and of those whose configuration is not specified.
(Node) structure_taxonomy_npclassifier_01pathway, ..._02superclass, ..._03class: the chemical classification of the structure by NPClassifier.
(Node) structure_taxonomy_classyfire_chemontid, ..._01kingdom, ..._02superclass, ..._03class, ..._04directparent: the chemical classification of the structure by ClassyFire.
(Node) organism_taxonomy_gbifid, organism_taxonomy_ncbiid, organism_taxonomy_ottid: the identifiers of the organism in GBIF, the NCBI taxonomy and the Open Tree of Life.
(Node) organism_taxonomy_01domain, ..._02kingdom, ..._03phylum, ..._04class, ..._05order, ..._06family, ..._07tribe, ..._08genus, ..._09species, ..._10varietas: the taxonomy of the organism (exports).
(Node) organism_id, organism_db_taxo, organism_taxon_ranks, organism_taxonomy (processed_*): the identifier of the organism in its taxonomic database, the name of the database, and the ranks and names of its lineage.
(Edge) reference_wikidata, reference_doi (exports): the Wikidata item and DOI of the reference.
(Edge) manual_validation (exports): the result of the manual validation of the pair (Y if it was validated by hand, empty otherwise).
(Edge) database (processed_*): the source database of the pair.
(Edge) organism_original, reference_original (processed_*): the organism and reference as given by the source database (the structures as given by the source databases, as InChI or SMILES strings, are left out, since they are long and the curated structure is given by the node).
(Edge) structure_original_type, reference_original_type (processed_*): the kind of the structure and reference identifiers of the source database (e.g. inchi, smiles, doi, pubmed, title).
(Edge) reference_doi, reference_pmcid, reference_pmid, reference_title (processed_*): the curated reference.

Tags

Biological Chemical Unweighted Bipartite Multigraph Metadata

Added

2026-10-31

Citation

A. Rutz, M. Sorokina, J. Galgonek, D. Mietchen, E. Willighagen, A. Gaudry, J. G. Graham, R. Stephan, R. Page, J. Vondrášek, C. Steinbeck, G. F. Pauli, J.-L. Wolfender, J. Bisson, P.-M. Allard, "The LOTUS initiative for open knowledge management in natural products research." eLife 11, e70780 (2022) 10.7554/eLife.70780 Sci-Hub

Upstream URL OK

https://lotus.naturalproducts.net/
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.5281/zenodo.5665294

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
2021_12_20	332,017	924,046	5.57	35.99	117.25	1890.15	-0.03	22	0.93	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	26.8 MiB	30.5 MiB	32.3 MiB	40.3 MiB
2022_02_08	331,556	923,940	5.57	36.01	117.49	1890.14	-0.03	22	0.93	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	32.0 MiB	36.9 MiB	38.6 MiB	50.3 MiB
2022_02_26	331,534	923,482	5.57	36.00	117.47	1890.12	-0.03	22	0.93	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	32.0 MiB	36.9 MiB	38.7 MiB	50.2 MiB
2022_03_18	260,508	718,968	5.52	30.40	105.18	1916.74	-0.04	24	0.92	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	28.4 MiB	33.4 MiB	35.1 MiB	47.1 MiB
2022_05_25	236,769	650,091	5.49	27.85	101.80	1201.52	-0.01	24	0.91	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	25.6 MiB	30.3 MiB	31.7 MiB	42.8 MiB
2022_07_01	256,700	683,597	5.33	29.35	103.02	3756.95	-0.04	26	0.91	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	27.9 MiB	32.9 MiB	34.5 MiB	46.4 MiB
2022_09_16	256,670	668,741	5.21	28.31	103.69	3747.26	-0.04	26	0.91	Undirected	Bipartite	is_structure wikidata name structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	27.9 MiB	32.8 MiB	34.4 MiB	46.2 MiB
2023_01_06	257,586	658,235	5.11	29.01	105.44	765.04	-0.04	24	0.92	Undirected	Bipartite	is_structure wikidata name structure_cid structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	28.7 MiB	34.4 MiB	36.1 MiB	47.5 MiB
2026_04_13	264,723	672,365	5.08	29.67	105.84	637.98	-0.04	26	0.92	Undirected	Bipartite	is_structure wikidata name structure_cid structure_exact_mass structure_inchi structure_inchikey structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2_d structure_stereocenters_total structure_stereocenters_unspecified structure_taxonomy_classyfire_01kingdom structure_taxonomy_classyfire_02superclass structure_taxonomy_classyfire_03class structure_taxonomy_classyfire_04directparent structure_taxonomy_classyfire_chemontid structure_taxonomy_npclassifier_01pathway structure_taxonomy_npclassifier_02superclass structure_taxonomy_npclassifier_03class structure_xlogp organism_taxonomy_01domain organism_taxonomy_02kingdom organism_taxonomy_03phylum organism_taxonomy_04class organism_taxonomy_05order organism_taxonomy_06family organism_taxonomy_07tribe organism_taxonomy_08genus organism_taxonomy_09species organism_taxonomy_10varietas organism_taxonomy_gbifid organism_taxonomy_ncbiid organism_taxonomy_ottid	reference_wikidata reference_doi manual_validation	30.8 MiB	37.6 MiB	39.6 MiB	56.4 MiB
processed_2021_05_28	317,601	3,477,571	21.90	158.47	114.20	2211.91	-0.03	24	0.93	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	60.1 MiB	72.6 MiB	73.3 MiB	108.4 MiB
processed_2021_12_20	338,694	6,438,722	38.02	289.05	126.44	1674.17	-0.03	22	0.93	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	63.5 MiB	75.8 MiB	76.4 MiB	99.8 MiB
processed_2022_03_23	268,165	5,731,021	42.74	342.67	115.58	2257.15	-0.03	24	0.92	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	54.4 MiB	65.3 MiB	65.8 MiB	85.7 MiB
processed_2022_05_25	264,278	6,467,819	48.95	328.86	110.35	4499.81	-0.04	24	0.91	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	54.5 MiB	66.8 MiB	67.4 MiB	87.1 MiB
processed_2022_07_01	265,901	6,660,406	50.10	387.92	110.71	4970.89	-0.03	24	0.91	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	55.2 MiB	67.6 MiB	68.2 MiB	87.0 MiB
processed_2022_09_16	264,401	6,273,974	47.46	337.69	111.65	4616.18	-0.03	24	0.91	Undirected	Bipartite	is_structure name structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	53.1 MiB	64.6 MiB	65.2 MiB	83.3 MiB
processed_2023_01_13	266,927	6,269,689	46.98	355.12	113.56	1168.66	-0.04	26	0.92	Undirected	Bipartite	is_structure name structure_cid structure_inchi structure_inchi_2d structure_inchikey structure_inchikey_2d structure_molecular_formula structure_name_iupac structure_smiles structure_smiles_2d structure_stereocenters_total structure_stereocenters_unspecified organism_db_taxo organism_id organism_taxon_ranks organism_taxonomy	database organism_original structure_original_type reference_original_type reference_original reference_doi reference_pmcid reference_pmid reference_title	54.5 MiB	66.8 MiB	67.3 MiB	86.0 MiB