2024-03-28T10:27:33Z
https://zenodo.org/oai2d
oai:zenodo.org:5802114
2022-04-28T08:45:32Z
software
user-the-lotus-initiative
Jonathan Bisson
Adriano Rutz
WhiteSource Renovate
Pierre-Marie Allard
2021-12-23
<p>Initial release</p>
https://doi.org/10.5281/zenodo.5802114
oai:zenodo.org:5802114
Zenodo
https://github.com/lotusnprod/lotus-wikidata-interact/tree/1.0.0
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5802113
info:eu-repo/semantics/openAccess
Other (Open)
lotusnprod/lotus-wikidata-interact: v1.0.0
info:eu-repo/semantics/other
oai:zenodo.org:10688056
2024-03-06T13:35:06Z
openaire_data
user-the-lotus-initiative
Marco, Visani
2024-02-21
<p>This file contains the wikidata taxonomy for each species present in the LOTUS databae. </p>
<p>For example <a href="https://w.wiki/9EWo" target="_blank" rel="noopener">this</a> will fetch the taxonomy of Homo sapiens on Wikidata. </p>
https://doi.org/10.5281/zenodo.10688056
oai:zenodo.org:10688056
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.10688055
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
LOTUS
Wikidata
Phylogeny
This archive contains the Wikidata taxonomy of each species present in the LOTUS database.
info:eu-repo/semantics/other
oai:zenodo.org:5802108
2022-05-25T20:56:39Z
software
user-the-lotus-initiative
Adriano Rutz
Jonathan Bisson
Pierre-Marie Allard
ArnaudGaudry
WhiteSource Renovate
2021-12-23
<p>Initial release</p>
https://doi.org/10.5281/zenodo.5802108
oai:zenodo.org:5802108
Zenodo
https://github.com/lotusnprod/lotus-processor/tree/1.0.0
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5802107
info:eu-repo/semantics/openAccess
Other (Open)
lotusnprod/lotus-processor: v1.0.0
info:eu-repo/semantics/other
oai:zenodo.org:5801808
2023-01-13T14:27:55Z
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
Gaudry, Arnaud
2021-12-20
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5801808
oai:zenodo.org:5801808
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801807
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
The LOTUS Initiative for Open Natural Products Research: TMAP
info:eu-repo/semantics/other
oai:zenodo.org:6873163
2022-07-21T13:48:47Z
openaire_data
user-the-lotus-initiative
Adriano Rutz
James Hare
2022-07-21
<p>The query (<a href="https://w.wiki/5UJq">https://w.wiki/5UJq</a>) was performed on 2022-07-18 and returned 2,887,803 rows.</p>
<p>A brief overview is available at <a href="https://adafede.github.io/wd-taxon-names/">https://adafede.github.io/wd-taxon-names/ </a></p>
https://doi.org/10.5281/zenodo.6873163
oai:zenodo.org:6873163
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6873162
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
taxon name
wikidata
query_5UJq
info:eu-repo/semantics/other
oai:zenodo.org:6471980
2022-05-27T12:43:50Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2022-03-23
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6471980
oai:zenodo.org:6471980
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:7085062
2023-01-13T14:28:12Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7085062
oai:zenodo.org:7085062
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6378223
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: metadata
info:eu-repo/semantics/other
oai:zenodo.org:6786307
2023-01-13T14:28:12Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-07-01
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.6786307
oai:zenodo.org:6786307
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6378223
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: metadata
info:eu-repo/semantics/other
oai:zenodo.org:6786337
2023-01-13T14:27:59Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-07-01
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.6786337
oai:zenodo.org:6786337
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:5668855
2023-01-13T14:28:16Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
Wikidata Community
2021-11-10
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p>
<p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p>
<p>This dataset is constituted of 4 tables.</p>
<ol>
<li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li>
<li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li>
<li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li>
<li>compound_reference_taxon.tsv - the documented structure-organism pairs</li>
</ol>
<p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p>
<p> </p>
<p><br>
</p>
https://doi.org/10.5281/zenodo.5668855
oai:zenodo.org:5668855
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5668854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
lotus
wikidata
The LOTUS Initiative for Open Natural Products Research: wikidata query results
info:eu-repo/semantics/other
oai:zenodo.org:6582124
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-05-25
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6582124
oai:zenodo.org:6582124
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6299673
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6299673
oai:zenodo.org:6299673
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:5794107
2023-03-29T20:32:17Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5794107
oai:zenodo.org:5794107
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6007029
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6007029
oai:zenodo.org:6007029
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6148914
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6148914
oai:zenodo.org:6148914
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6582123
2023-01-13T14:28:06Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-05-25
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6582123
oai:zenodo.org:6582123
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6786325
2023-01-13T14:28:07Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-07-01
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6786325
oai:zenodo.org:6786325
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6378193
2023-01-13T14:27:59Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-03-23
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6378193
oai:zenodo.org:6378193
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:7085066
2023-01-13T14:28:00Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7085066
oai:zenodo.org:7085066
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:5793668
2023-01-13T14:27:58Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5793668
oai:zenodo.org:5793668
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:5794597
2023-01-13T14:28:04Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.5794597
oai:zenodo.org:5794597
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:7124055
2023-07-23T16:53:29Z
openaire_data
user-the-lotus-initiative
Kuhn, Stefan
Nuzillard, Jean-Marc
2022-09-29
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 9</a> .</p>
<p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p>
<p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p>
<p>File 220916_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/7085063">the LOTUS database version 9</a> and the SMILES chains of the compounds were collected.</p>
<p>The SMILES chains were translated to 2D chemical structures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p>
<p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p>
<p>Each compound was also supplemented with metadata from file 220916_frozen_metadata.csv .</p>
<p>Archive file acd_lotusv9.sdf.zip contains acd_lotusv9.sdf with 218,478 compound descriptions inside.</p>
<p>The description of the first compound was copied in file firstmolv9.sdf and is provided for a quick inspection of the database content.</p>
<p>The title line in firstmolv9.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220916_frozen_metadata.csv .</p>
<p>File acd_lotusv9.sdf contains biological taxonomy data from file 220916_frozen_metadata.csv that were not exploited in acd_lotusv7. Sub-files dealing with a particular taxon can be easily produced now.</p>
<p>Chemical shift calculations for <sup>13</sup>C nuclei using the HOSE code approach are available <a href="https://zenodo.org/record/7047760">here</a> for the compounds in acd_lotusv7.</p>
<p> </p>
https://doi.org/10.5281/zenodo.7124055
oai:zenodo.org:7124055
eng
Zenodo
https://zenodo.org/record/6582124
https://www.mdpi.com/1420-3049/26/3/637
https://elifesciences.org/articles/70780
https://github.com/rdkit/rdkit
https://www.mdpi.com/2673-4532/2/3/6
https://www.wikidata.org/
https://chemrxiv.org/engage/chemrxiv/article-details/62b03c51f70c21fdc1350d90
https://nuzillard.github.io/acd_lotus/acd_lotusv7.mp4
https://nuzillard.github.io/acd_lotus/acd_lotusv7_fr.mp4
https://pubs.acs.org/doi/10.1021/acsomega.9b00488
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6621129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Natural product chemistry
Nuclear Magnetic Resonance
NMR
Chemical shift prediction
Biological taxonomy
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
info:eu-repo/semantics/other
oai:zenodo.org:8287341
2023-08-28T14:26:54Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
Jonathan Bisson
Adriano Rutz
2023-08-27
<p>An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (<a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780)</a>.<br>
Fragmented using cfm-predict 4 (<a href="https://doi.org/10.1021/acs.analchem.1c01465">https://doi.org/10.1021/acs.analchem.1c01465</a>) .</p>
<p>In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> <a href="https://doi.org/10.1021/ACS.ANALCHEM.5B04804">https://doi.org/10.1021/ACS.ANALCHEM.5B04804</a></p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_builder">https://github.com/mandelbrot-project/spectral_lib_builder</a> for associated building scripts.</p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_matcher">https://github.com/mandelbrot-project/spectral_lib_matcher</a> for associated matching scripts.</p>
<p>The <a href="https://docs.python.org/3/library/pickle.html#module-pickle">pickle</a> formated ISDBs are build for quicker loading via matchms.</p>
https://doi.org/10.5281/zenodo.8287341
oai:zenodo.org:8287341
Zenodo
https://doi.org/10.5281/zenodo.6786307
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5607185
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
spectral databases
LOTUS
mass spectrometry
ISDB: In Silico Spectral Databases of Natural Products
info:eu-repo/semantics/other
oai:zenodo.org:5607264
2023-08-27T15:08:59Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
Jonathan Bisson
Adriano Rutz
2021-10-28
<p>An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative.</p>
<p>This spectral file is in positive ionisation mode only. Fragmented using cfm-predict 3.0 <a href="https://cfmid.wishartlab.com/">https://cfmid.wishartlab.com/</a></p>
<p>Intensities at the low, medium and high energy level have been meaned.</p>
<p> </p>
<p>In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> <a href="https://doi.org/10.1021/ACS.ANALCHEM.5B04804">https://doi.org/10.1021/ACS.ANALCHEM.5B04804</a></p>
<p>See <a href="http://oolonek.github.io/ISDB/">http://oolonek.github.io/ISDB/</a> for associated spectral matching scripts</p>
<p>LOTUS Initiative initially described in <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.5607264
oai:zenodo.org:5607264
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5607185
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
spectral databases
LOTUS
mass spectrometry
ISDB: In Silico Spectral Databases of Natural Products
info:eu-repo/semantics/other
oai:zenodo.org:7534059
2023-01-13T14:27:57Z
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
Gaudry, Arnaud
2022-09-16
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7534059
oai:zenodo.org:7534059
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801807
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
The LOTUS Initiative for Open Natural Products Research: TMAP
info:eu-repo/semantics/other
oai:zenodo.org:6787294
2023-01-13T14:27:55Z
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
Gaudry, Arnaud
2022-07-01
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.6787294
oai:zenodo.org:6787294
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801807
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
The LOTUS Initiative for Open Natural Products Research: TMAP
info:eu-repo/semantics/other
oai:zenodo.org:7085067
2023-01-13T14:27:56Z
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
Gaudry, Arnaud
2022-09-16
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7085067
oai:zenodo.org:7085067
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801807
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
The LOTUS Initiative for Open Natural Products Research: TMAP
info:eu-repo/semantics/other
oai:zenodo.org:5793224
2023-01-13T14:28:16Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
Wikidata Community
2021-12-20
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p>
<p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p>
<p>This dataset is constituted of 4 tables.</p>
<ol>
<li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li>
<li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li>
<li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li>
<li>compound_reference_taxon.tsv - the documented structure-organism pairs</li>
</ol>
<p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p>
<p> </p>
<p><br>
</p>
https://doi.org/10.5281/zenodo.5793224
oai:zenodo.org:5793224
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5668854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
lotus
wikidata
The LOTUS Initiative for Open Natural Products Research: wikidata query results
info:eu-repo/semantics/other
oai:zenodo.org:6042345
2023-01-13T14:28:05Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-02-08
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6042345
oai:zenodo.org:6042345
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6277266
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-12-20
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6277266
oai:zenodo.org:6277266
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6378204
2023-03-29T20:32:18Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-03-23
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6378204
oai:zenodo.org:6378204
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:7085063
2023-03-29T20:32:19Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7085063
oai:zenodo.org:7085063
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:6148819
2023-01-13T14:28:05Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-02-08
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6148819
oai:zenodo.org:6148819
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6378203
2023-01-13T14:28:06Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-03-23
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6378203
oai:zenodo.org:6378203
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:7085064
2023-01-13T14:28:07Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.7085064
oai:zenodo.org:7085064
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6487114
2022-05-27T12:43:51Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2022-03-23
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6487114
oai:zenodo.org:6487114
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:5801816
2022-05-27T12:43:49Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2021-12-20
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5801816
oai:zenodo.org:5801816
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:6007004
2022-05-27T12:43:50Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2022-03-23
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6007004
oai:zenodo.org:6007004
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:7534077
2023-01-14T02:26:40Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7534077
oai:zenodo.org:7534077
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6378223
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: metadata
info:eu-repo/semantics/other
oai:zenodo.org:6621130
2023-07-23T16:53:28Z
openaire_data
user-the-lotus-initiative
Nuzillard, Jean-Marc
2022-06-07
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 7</a> .</p>
<p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p>
<p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p>
<p>File 220525_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/6582124">the LOTUS database version 7</a> and the SMILES chains of the compounds were collected.</p>
<p>The SMILES chains were translated to 2D chemical strucures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p>
<p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p>
<p>Each compound was also supplemented with metadata from file 220525_frozen_metadata.csv .</p>
<p>Archive file acd_lotusv7.zip contains acd_lotusv7.sdf with 201,010 compound descriptions inside.</p>
<p>The description of the first compound was copied in file firstmol.sdf and is provided for a quick inspection of the database content.</p>
<p>The title line in firstmol.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220525_frozen_metadata.csv .</p>
https://doi.org/10.5281/zenodo.6621130
oai:zenodo.org:6621130
eng
Zenodo
https://zenodo.org/record/6582124
https://www.mdpi.com/1420-3049/26/3/637
https://elifesciences.org/articles/70780
https://github.com/rdkit/rdkit
https://www.mdpi.com/2673-4532/2/3/6
https://www.wikidata.org/
https://chemrxiv.org/engage/chemrxiv/article-details/62b03c51f70c21fdc1350d90
https://nuzillard.github.io/acd_lotus/acd_lotusv7.mp4
https://nuzillard.github.io/acd_lotus/acd_lotusv7_fr.mp4
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6621129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Natural product chemistry
Nuclear Magnetic Resonance
NMR
Chemical shift prediction
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
info:eu-repo/semantics/other
oai:zenodo.org:6378196
2023-01-13T14:28:05Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-03-23
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.6378196
oai:zenodo.org:6378196
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:7047760
2023-07-23T16:53:28Z
openaire_data
user-the-lotus-initiative
Kuhn, Stefan
Nuzillard, Jean-Marc
2022-09-04
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 7</a> .</p>
<p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p>
<p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p>
<p>File 220525_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/6582124">the LOTUS database version 7</a> and the SMILES chains of the compounds were collected.</p>
<p>The SMILES chains were translated to 2D chemical strucures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p>
<p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p>
<p>Each compound was also supplemented with metadata from file 220525_frozen_metadata.csv .</p>
<p>Archive file acd_lotusv7.zip contains acd_lotusv7.sdf with 201,010 compound descriptions inside.</p>
<p>The description of the first compound was copied in file firstmol.sdf and is provided for a quick inspection of the database content.</p>
<p>The title line in firstmol.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220525_frozen_metadata.csv .</p>
<p>Archive file hose_lotusv7.zip contains hose_lotusv7.sdf with 201,021 compound descriptions inside, from the LOTUS database. The chemical shift values were predicted by means of the HOSE-code-based <sup>13</sup>C NMR chemical shifts predictor in <a href="https://nmrshiftdb.nmr.uni-koeln.de">nmrshiftdb2</a> . More details are given in the <a href="https://sourceforge.net/p/nmrshiftdb2/wiki/PredictorJars/">nmrshiftdb2 wiki</a> and in a <a href="https://doi.org/10.1021/acsomega.9b00488">publication</a> .</p>
https://doi.org/10.5281/zenodo.7047760
oai:zenodo.org:7047760
eng
Zenodo
https://zenodo.org/record/6582124
https://www.mdpi.com/1420-3049/26/3/637
https://elifesciences.org/articles/70780
https://github.com/rdkit/rdkit
https://www.mdpi.com/2673-4532/2/3/6
https://www.wikidata.org/
https://chemrxiv.org/engage/chemrxiv/article-details/62b03c51f70c21fdc1350d90
https://nuzillard.github.io/acd_lotus/acd_lotusv7.mp4
https://nuzillard.github.io/acd_lotus/acd_lotusv7_fr.mp4
https://pubs.acs.org/doi/10.1021/acsomega.9b00488
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6621129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Natural product chemistry
Nuclear Magnetic Resonance
NMR
Chemical shift prediction
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
info:eu-repo/semantics/other
oai:zenodo.org:7534250
2023-08-27T15:08:59Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
Jonathan Bisson
Adriano Rutz
2022-07-29
<p>An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (<a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780)</a>.<br>
Fragmented using cfm-predict 4 (<a href="https://doi.org/10.1021/acs.analchem.1c01465">https://doi.org/10.1021/acs.analchem.1c01465</a>) .</p>
<p>In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> <a href="https://doi.org/10.1021/ACS.ANALCHEM.5B04804">https://doi.org/10.1021/ACS.ANALCHEM.5B04804</a></p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_builder">https://github.com/mandelbrot-project/spectral_lib_builder</a> for associated building scripts.</p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_matcher">https://github.com/mandelbrot-project/spectral_lib_matcher</a> for associated matching scripts.</p>
https://doi.org/10.5281/zenodo.7534250
oai:zenodo.org:7534250
Zenodo
https://doi.org/10.5281/zenodo.6786307
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5607185
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
spectral databases
LOTUS
mass spectrometry
ISDB: In Silico Spectral Databases of Natural Products
info:eu-repo/semantics/other
oai:zenodo.org:7085065
2023-01-13T14:28:06Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.7085065
oai:zenodo.org:7085065
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:6939173
2023-08-27T15:08:59Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
Jonathan Bisson
Adriano Rutz
2022-07-29
<p>An In Silico spectral DataBase (<strong>ISDB</strong>) of natural products calculated from structures aggregated in the frame of the LOTUS Initiative (<a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780)</a>.<br>
Fragmented using cfm-predict 4 (<a href="https://doi.org/10.1021/acs.analchem.1c01465">https://doi.org/10.1021/acs.analchem.1c01465</a>) .</p>
<p>In silico spectral database preparation and use for dereplication initially described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> <a href="https://doi.org/10.1021/ACS.ANALCHEM.5B04804">https://doi.org/10.1021/ACS.ANALCHEM.5B04804</a></p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_builder">https://github.com/mandelbrot-project/spectral_lib_builder</a> for associated building scripts.</p>
<p>See <a href="https://github.com/mandelbrot-project/spectral_lib_matcher">https://github.com/mandelbrot-project/spectral_lib_matcher</a> for associated matching scripts.</p>
https://doi.org/10.5281/zenodo.6939173
oai:zenodo.org:6939173
Zenodo
https://doi.org/10.5281/zenodo.6786307
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5607185
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
spectral databases
LOTUS
mass spectrometry
ISDB: In Silico Spectral Databases of Natural Products
info:eu-repo/semantics/other
oai:zenodo.org:6582346
2022-05-26T01:50:44Z
software
user-the-lotus-initiative
Adriano Rutz
Jonathan Bisson
Pierre-Marie Allard
Arnaud Gaudry
2022-05-25
<p>What's Changed</p>
<ul>
<li>Update plugin com.github.johnrengelman.shadow to v7.1.2 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/15">https://github.com/lotusnprod/lotus-processor/pull/15</a></li>
<li>Update dependency gradle to v7.4 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/19">https://github.com/lotusnprod/lotus-processor/pull/19</a></li>
<li>Update actions/setup-java action to v3 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/23">https://github.com/lotusnprod/lotus-processor/pull/23</a></li>
<li>Update actions/checkout action to v3 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/24">https://github.com/lotusnprod/lotus-processor/pull/24</a></li>
<li>Update dependency gradle to v7.4.1 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/26">https://github.com/lotusnprod/lotus-processor/pull/26</a></li>
<li>Update dependency gradle to v7.4.2 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/27">https://github.com/lotusnprod/lotus-processor/pull/27</a></li>
<li>Update plugin org.jetbrains.kotlin.jvm to v1.6.20 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/28">https://github.com/lotusnprod/lotus-processor/pull/28</a></li>
<li>Update plugin org.jetbrains.kotlin.jvm to v1.6.21 by @renovate in <a href="https://github.com/lotusnprod/lotus-processor/pull/30">https://github.com/lotusnprod/lotus-processor/pull/30</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/lotusnprod/lotus-processor/compare/1.0.0...1.1.0">https://github.com/lotusnprod/lotus-processor/compare/1.0.0...1.1.0</a></p>
https://doi.org/10.5281/zenodo.6582346
oai:zenodo.org:6582346
Zenodo
https://github.com/lotusnprod/lotus-processor/tree/1.1.0
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5802107
info:eu-repo/semantics/openAccess
Other (Open)
lotusnprod/lotus-processor: v1.1.0
info:eu-repo/semantics/other
oai:zenodo.org:6378388
2023-01-13T14:27:55Z
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
Gaudry, Arnaud
2022-03-23
<p>TMAP of the compounds present on Wikidata curated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6378388
oai:zenodo.org:6378388
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801807
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
The LOTUS Initiative for Open Natural Products Research: TMAP
info:eu-repo/semantics/other
oai:zenodo.org:5802120
2022-04-28T08:45:32Z
software
user-the-lotus-initiative
Maria Sorokina
Adriano Rutz
WhiteSource Renovate
Egon Willighagen
Imgbot
2021-12-23
<p>Not really the initial release</p>
https://doi.org/10.5281/zenodo.5802120
oai:zenodo.org:5802120
Zenodo
https://github.com/lotusnprod/lotus-web/tree/1.0.0
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5802119
info:eu-repo/semantics/openAccess
Other (Open)
lotusnprod/lotus-web: v1.0.0
info:eu-repo/semantics/other
oai:zenodo.org:6582125
2023-01-13T14:28:11Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-05-25
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6582125
oai:zenodo.org:6582125
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6378223
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: metadata
info:eu-repo/semantics/other
oai:zenodo.org:6378224
2023-01-13T14:28:11Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-03-23
<p>Metadata of each of the three objects (structures, organisms, references) used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6378224
oai:zenodo.org:6378224
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6378223
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: metadata
info:eu-repo/semantics/other
oai:zenodo.org:5801799
2022-05-27T12:43:49Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2021-12-20
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5801799
oai:zenodo.org:5801799
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:5807826
2022-05-27T12:43:50Z
openaire_data
user-the-lotus-initiative
Bisson, Jonathan
Allard, Pierre-Marie
Rutz, Adriano
2021-12-20
<p>Custom dictionaries created in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5807826
oai:zenodo.org:5807826
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5801798
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dictionaries
The LOTUS Initiative for Open Natural Products Research: custom dictionaries
info:eu-repo/semantics/other
oai:zenodo.org:5665295
2023-01-13T14:27:58Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2021-05-28
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.5665295
oai:zenodo.org:5665295
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: dataset
info:eu-repo/semantics/other
oai:zenodo.org:7534062
2023-01-14T02:26:40Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7534062
oai:zenodo.org:7534062
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:7534083
2023-01-14T02:26:39Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
Wikidata Community
2022-09-16
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p>
<p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p>
<p>This dataset is constituted of 4 tables.</p>
<ol>
<li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li>
<li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li>
<li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li>
<li>compound_reference_taxon.tsv - the documented structure-organism pairs</li>
</ol>
<p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p>
<p> </p>
<p><br>
</p>
https://doi.org/10.5281/zenodo.7534083
oai:zenodo.org:7534083
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5668854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
lotus
wikidata
The LOTUS Initiative for Open Natural Products Research: wikidata query results
info:eu-repo/semantics/other
oai:zenodo.org:7534070
2023-01-14T02:26:39Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.7534070
oai:zenodo.org:7534070
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6007177
2023-01-13T14:28:05Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-02-08
<p>Biological and chemical trees made from frozen metadata (<a href="https://doi.org/10.5281/zenodo.5794106">10.5281/zenodo.5794106</a>) (for example, for PubChem)</p>
https://doi.org/10.5281/zenodo.6007177
oai:zenodo.org:6007177
Zenodo
https://doi.org/10.5281/zenodo.5794106
https://doi.org/10.1101/2021.02.28.433265
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6007176
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
taxonomy
The LOTUS Initiative for Open Natural Products Research: biological and chemical trees
info:eu-repo/semantics/other
oai:zenodo.org:6582121
2023-01-13T14:27:59Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-05-25
<p>Dataset used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
https://doi.org/10.5281/zenodo.6582121
oai:zenodo.org:6582121
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5665294
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset
info:eu-repo/semantics/other
oai:zenodo.org:5668380
2022-04-28T08:45:34Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
2021-11-10
<p>Output of wikidata SPARQL query <a href="https://w.wiki/4N8G">https://w.wiki/4N8G</a> realized on the 2021-11-10T16:56</p>
<pre>
</pre>
https://doi.org/10.5281/zenodo.5668380
oai:zenodo.org:5668380
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5668379
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
lotus
sparql
wikidata
query_4N8G_202111101656
info:eu-repo/semantics/other
oai:zenodo.org:6786314
2023-03-29T20:32:19Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-07-01
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.6786314
oai:zenodo.org:6786314
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:7534071
2023-03-29T20:32:20Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2023-01-06
<p>Dataset present on Wikidata used in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
https://doi.org/10.5281/zenodo.7534071
oai:zenodo.org:7534071
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.5281/zenodo.5793224
https://doi.org/10.5281/zenodo.5793668
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794106
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
wikidata
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata)
info:eu-repo/semantics/other
oai:zenodo.org:7085061
2023-01-13T14:28:16Z
openaire_data
user-the-lotus-initiative
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
Wikidata Community
2022-09-16
<p>Wikidata query results returned by the downloadLotus module of the <a href="https://github.com/lotusnprod/lotus-wikidata-interact">https://github.com/lotusnprod/lotus-wikidata-interact</a> program.</p>
<p>See details of the module here <a href="https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md">https://github.com/lotusnprod/lotus-wikidata-interact/blob/main/downloadLotus/README.md</a></p>
<p>This dataset is constituted of 4 tables.</p>
<ol>
<li>compounds.tsv - chemical structures metadata (wikidataId, canonicalSmiles, isomericSmiles, inchi, inchiKey)</li>
<li>references.tsv - bibliographical references metadata (wikidataId, pipe separated DOIs, titles)</li>
<li>taxa.tsv - biological organisms metadata (wikidataId, pipe separated names, taxa rank)</li>
<li>compound_reference_taxon.tsv - the documented structure-organism pairs</li>
</ol>
<p>This dataset includes not only the outputs of the LOTUS processing pipeline (available here <a href="https://doi.org/10.5281/zenodo.5665295">https://doi.org/10.5281/zenodo.5665295</a> ) but also any of wikidata chemical compounds having the found in taxon property (<a href="https://www.wikidata.org/wiki/Property:P703">https://www.wikidata.org/wiki/Property:P703</a>) and their associated organisms and documenting references.</p>
<p> </p>
<p><br>
</p>
https://doi.org/10.5281/zenodo.7085061
oai:zenodo.org:7085061
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5668854
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
lotus
wikidata
The LOTUS Initiative for Open Natural Products Research: wikidata query results
info:eu-repo/semantics/other
oai:zenodo.org:7534069
2023-01-14T02:26:41Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-09-16
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.7534069
oai:zenodo.org:7534069
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:6786330
2023-01-13T14:28:06Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-07-01
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.7554/eLife.70780">https://doi.org/10.7554/eLife.70780</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.6786330
oai:zenodo.org:6786330
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:6582122
2023-01-13T14:28:05Z
openaire_data
user-the-lotus-initiative
Sorokina, Maria
Galgonek, Jakub
Mietchen, Daniel
Willighagen, Egon
Gaudry, Arnaud
Graham, James G.
Stephan, Ralf
Page, Roderic
Vondrášek, Jiří
Steinbeck, Christoph
Pauli, Guido F.
Wolfender, Jean-Luc
Rutz, Adriano
Bisson, Jonathan
Allard, Pierre-Marie
2022-05-25
<p>Dataset not uploaded to Wikidata. </p>
<p>Generated in the frame of the LOTUS Initiative: <a href="https://doi.org/10.1101/2021.02.28.433265">https://doi.org/10.1101/2021.02.28.433265</a></p>
<p>Shared for further curation.</p>
https://doi.org/10.5281/zenodo.6582122
oai:zenodo.org:6582122
Zenodo
https://doi.org/10.1101/2021.02.28.433265
https://doi.org/10.7554/eLife.70780
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5794596
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
The LOTUS Initiative for Open Natural Products Research: waste to recycle
info:eu-repo/semantics/other
oai:zenodo.org:5607186
2023-08-27T15:08:59Z
openaire_data
user-the-lotus-initiative
Pierre-Marie Allard
Jonathan Bisson
2021-10-28
<p>An In Silico spectral DataBase (ISDB) of natural products initially calculated from the Universal Natural Products Database (UNPD).</p>
<p>This spectral file is in positive ionisation mode only. Fragmented using cfm-predict 2.0 <a href="https://sourceforge.net/projects/cfm-id/">https://sourceforge.net/projects/cfm-id/</a></p>
<p> </p>
<p>Originally described in <em>Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication</em> <a href="https://doi.org/10.1021/ACS.ANALCHEM.5B04804">https://doi.org/10.1021/ACS.ANALCHEM.5B04804</a></p>
<p> </p>
<p>See <a href="http://oolonek.github.io/ISDB/">http://oolonek.github.io/ISDB/</a> for associated scripts</p>
https://doi.org/10.5281/zenodo.5607186
oai:zenodo.org:5607186
Zenodo
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.5607185
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
natural products
metabolomics
metabolite annotation
spectral databases
ISDB: In Silico Spectral Databases of Natural Products
info:eu-repo/semantics/other
oai:zenodo.org:8175939
2023-07-25T02:26:59Z
openaire_data
user-the-lotus-initiative
Kuhn, Stefan
Nuzillard, Jean-Marc
2023-07-23
<p>A structure database of natural products in SDF format was created from <a href="https://zenodo.org/record/6582124">the LOTUS database version 9</a> .</p>
<p>This database is intended to facilitate the <a href="https://www.mdpi.com/1420-3049/26/3/637">dereplication of natural products</a>.</p>
<p>The LOTUS database was described in <a href="https://elifesciences.org/articles/70780">this publication</a> (free download).</p>
<p>File 220916_frozen_metadata.csv was downloaded from <a href="https://zenodo.org/record/7085063">the LOTUS database version 9</a> and the SMILES chains of the compounds were collected.</p>
<p>The SMILES chains were translated to 2D chemical structures using python scripts relying on the <a href="https://github.com/rdkit/rdkit">RDKit</a> library.</p>
<p>Each compound was associated to predicted <sup>13</sup>C NMR chemical shifts by means of an already reported <a href="https://www.mdpi.com/2673-4532/2/3/6">procedure</a> (free download).</p>
<p>Each compound was also supplemented with metadata from file 220916_frozen_metadata.csv .</p>
<p>Archive file acd_lotusv9.sdf.zip contains acd_lotusv9.sdf with 218,478 compound descriptions inside.</p>
<p>Archive file acd_lotusv9.NMRUDB.zip is a compressed version of acd_lotusv9.NMRUDB, itself created by importation of file acd_lotusv9.sdf in an ACD/Labs database file (new with version 0.0.4).</p>
<p>The description of the first compound was copied in file firstmolv9.sdf and is provided for a quick inspection of the database content.</p>
<p>The title line in firstmolv9.sdf is Q43656_2, meaning that more data about this compound may be found by searching in <a href="https://www.wikidata.org/">Wikidata</a> for Q43656 and that the initial data was given by line 2 in file 220916_frozen_metadata.csv .</p>
<p>Files acd_lotusv9.sdf acd_lotusv9.NMRUDB contain biological taxonomy data from file 220916_frozen_metadata.csv that were not exploited in acd_lotusv7. Sub-files dealing with a particular taxon can be easily produced now.</p>
<p>Chemical shift calculations for <sup>13</sup>C nuclei using the HOSE code approach are available <a href="https://zenodo.org/record/7047760">here</a> for the compounds in acd_lotusv7.</p>
<p> </p>
https://doi.org/10.5281/zenodo.8175939
oai:zenodo.org:8175939
eng
Zenodo
https://zenodo.org/record/6582124
https://www.mdpi.com/1420-3049/26/3/637
https://elifesciences.org/articles/70780
https://github.com/rdkit/rdkit
https://www.mdpi.com/2673-4532/2/3/6
https://www.wikidata.org/
https://chemrxiv.org/engage/chemrxiv/article-details/62b03c51f70c21fdc1350d90
https://nuzillard.github.io/acd_lotus/acd_lotusv7.mp4
https://nuzillard.github.io/acd_lotus/acd_lotusv7_fr.mp4
https://pubs.acs.org/doi/10.1021/acsomega.9b00488
https://zenodo.org/communities/the-lotus-initiative
https://doi.org/10.5281/zenodo.6621129
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Natural product chemistry
Nuclear Magnetic Resonance
NMR
Chemical shift prediction
Biological taxonomy
Natural products structure database LOTUS supplemented with predicted 13C NMR chemical shifts.
info:eu-repo/semantics/other