How and where can erroneous entries in the Lotus database be reported and corrected? For example mescaline has an entry of being reported from Echinopsis spachianus. If a person is familiar with the reference that is included, that paper specifically did not observe mescaline in this species (either in their experimental subjects or in their controls). This is only one example of erroneous data that would benefit from correction.

I tried dragging a molecular structure image displayed in the page into the search box to search. It accepted the search as a string (data:image/png;base64,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)

But on clicking search, it gave an error. It is repeatable.

So, i have an organism and i want to download all the chemical compounds related to that organism with their smile ID and the species that produce those chemical compounds.

So what i did was just search in the web page and found all the entries of chemical compounds related to that organism. And downloaded the SDF file which was the only downloading option available. And later converted it to excel format.

But what i realized was that file was missing compound names.

So what i wanted was Compound name, Smile ID, Species it is present.

Is is possible to get it as such from the LOTUS database by any means ?

Will facilitate reuse

When done, document it

to make it easier for potential contributors to find their way.

While I was reading this nice document, I imagine something that might be a cool feature: similarity/substructure networks of the structures color coded by taxonomy.
Let me know if that make sense for you to add.
Thanks

Hello:
I want to use Lotus to reconstruct evolution of natural products on phylogenetic trees. I began entering some references and taxon:compound pairs that are not in Lotus (or Wikidata) and found some unexpected complications and/or inconsistencies on how the taxon: compound and name:compound mapping depicted in Lotus in encoded in Wikidata and how these associations can be retrieved using queries of Wikidata. Can you help me understand what is happening so that I can add and retrieve data effectively? Thank you! Tanya

I give as example the compound blepharin (Q105216729 on Wikidata).

1. If you query "blepharin" in Lotus, you get no results.
2. If you query the InChIKey encoding of blepharin, "PYQSUTLVBSTCSK-UHFFFAOYSA-N", in Lotus, you get "Q105216729
2-[(3-hydroxy-2h-1,4-benzoxazin-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol".
3. That name "2-[(3-hydroxy-2h-1,4-benzoxazin-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol" does not appear in the Wikidata (nor PubChem) record for "blepharin". "Blepharin" does not occur in the Lotus record for "2-[(3-hydroxy-2h-1,4-benzoxazin-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol". Why not? Where is this name coming from, and why doesn't the name in the Wikidata record appear on Lotus (and vice versa)?
4. The chemical structure illustrated on Lotus for Q105216729 is not the same as chemical structure illustrated on PubChem for PubChem CID 14605136 (blepharin). PubChem has the structure depicted with N-C(=O). Lotus has the structure illustrated with N=C(-OH). Are these the same structure?
5. When you look at the Wikidata record for blepharin (Q105216729), you do not see the taxa listed on Lotus as containing this compound (record Q105216729 on Lotus). There is no "found in taxon P703" statement in the Wikidata record for the species listed on Lotus: Acanthus montanus, Blepharis edulis, Acanthus ebracteatus .
6. When you click on the Wikidata symbol for the reference for each of these taxon records in Lotus, you will see that the species name and the compound name "blepharin" both occur in the "main subject P921" statement for the reference (Q42783412) on Wikidata. This seems a dangerous way to make the taxon:compound link since a publication may has as its "main subject" multiple species and multiple compounds, but all combinations of them do not necessarily occur. How many of the taxon:compound links in Lotus are made via this "main subject" statement in the reference? Is there a plan to transfer these links to "found in taxon P703" statements on the compound Wikidata record?
7. When I query Wikidata for all compounds in, e.g. Acanthus montanus (Q4672080), it does not return blepharin (Q105216729). The query yields 10 compounds. See query text below.

SELECT DISTINCT ?taxon ?children ?childrenLabel ?structure ?structureLabel ?structure_inchi
WHERE {
VALUES ?taxon {
wd:Q4672080 # You can remove the Qxxxxxx and hit Ctrl+space, type the first letters and it should autocomplete
}
?children (wdt:P171*) ?taxon. # Include children taxa
?structure wdt:P234 ?structure_inchi ; # Get the InChI
(p:P703/ps:P703) ?children. # Found in given taxon/taxa

SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }}

8. When I query Lotus for the text string "Acanthus montanus", the query returns 16 compounds, including Q105216729. How can I retrieve the Lotus result from Wikidata?

Diethyl Phthalate is listed as naturally sourced, but it is widely considered an artifact of purification/isolation in natural product.

While this is one of the most common example, there are probably more, it could be interesting to have a way to flag compounds with dubious origin for manual review.

I want to connect to the local Docker instance of Lotus, so I can run the API query below. How do I do that?
I have both the mongo and lotus-online containers running, but I only see command line access via the Docker dashboard.

https://lotus.naturalproducts.net/api/search/simple?query=inchikey

Hello,

I wanna build a mongodb with LOTUS, but I cannot find the docker-compose.yml mentioned in the readme file, like "In the directory containing the 'docker-compose.yml' file run the following commands".

Could you send me the yml file by email: [email protected]?

Thank you!

I was wondering about your use of NPASS as a data source as I've found a variety of inconsistencies with it in the past:

• Found a few strange cases where '0' was given at the beginning of a name and should be replaced by 'No' e.g. https://bidd.group/NPASS/organism.php?org_id=NPO17300
• Chloroquine (https://bidd.group/NPASS/compound.php?compoundID=NPC476464) is listed as derived from lots of species that I believe to be incorrect e.g. Vernonia brachycalyx, with reference https://pubmed.ncbi.nlm.nih.gov/9170288/
• Inaccuracies at the level of biological activities of compounds e.g. Ivermectin is listed as having antiplasmodial activity (https://bidd.group/NPASS/compound.php?compoundID=NPC469812) but the given references are unrelated and I'm struggling to find references that support the given values.

NPASS is listred as a source in your paper, so wondering if you had vetted these issues somehow as I also notice that the choloroquine/Vernonia brachycalyx issue isn't apparent in LOTUS

I want to clarify the role of WikiData in LOTUS. Initially I thought LOTUS had curated a lot of sturcture-organism data which is then disseminated via https://lotus.naturalproducts.net and also via WikiData and that WikiData's role was simply dissemination. If this is the case, is it possible to extract only LOTUS-curated data from WikiData?

I suspect this isn't the case, as reading further the favoured approach to adding data to LOTUS is to add entries to WikiData directly. In this case, is there any distinction between LOTUS data and WikiData data?

When trying to open the SDF file, downloaded after a similarity search with SMILES (returning ~ 200 molecules), the SDF file cannot be opened (bad file), neither with R, nor with a user interface chemical program, like ChemDraw.

> read.SDFset(sdf_file_path)
An instance of "SDFset" with 1 molecules
There were 26 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In FUN(X[[i]], ...) : bad key value pair found:
									  V3000
2: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
3: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
4: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
5: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
6: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
7: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
8: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
9: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
10: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
11: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
12: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
13: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
14: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
15: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
16: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
17: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
18: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
19: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
20: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
21: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
22: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
23: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0
24: In FUN(X[[i]], ...) : bad key value pair found:
									  0 0 V3000
25: In mde(x) : NAs introduced by coercion
26: In read.SDFset(sdf_file_path) :
  1 invalid SDFs detected. To fix, run: valid <- validSDF(sdfset); sdfset <- sdfset[valid]


> validSDF(sdf_file_path)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘atomblock’ for signature ‘"character"’
In addition: Warning message:
In validSDF(sdf_file_path) : x needs to be of class SDFset

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I've downloaded some metabolite data from LOTUS and am trying to cross reference this with data from ChemBL. It seems that one of the more reliable ways to do this would be to use the SMILES key.

Looking at some examples in LOTUS e.g. https://lotus.naturalproducts.net/compound/lotus_id/LTS0095286, the SMILES given by Wikidata are (canonical) "COC1=CC2=C(C=CN=C2C=C1)C(C3CC4CCN3CC4C=C)O" and (isomeric) "COC1=CC2=C(C=CN=C2C=C1)C@HO", neither of which appear to provide a direct match in ChemBL. In contrast, the 2D Smiles given by lotus for this metbolite "C=CC1CN2CCC1CC2C(O)c1ccnc2ccc(OC)cc12" matches with the ChemBL compound (https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL15088/).

This 2D smiles given by LOTUS appears in general to match with chembl, and seems to be the result of applying the rdkit method: Chem.CanonSmiles(x) to the 'canonical' smiles given in Wikidata. My question is it possible to download this 2D SMILES directly and if not, is my guess as to how it is generated correct?

Note, I'm downloading the data using the query:

SELECT DISTINCT ?structure ?structureLabel ?structure_smiles ?structure_cas ?structure_inchikey ?organism ?organism_name WHERE {
VALUES ?taxon {
  wd:Q21754 # Gentianales
}
?organism (wdt:P171*) ?taxon;
  wdt:P225 ?organism_name.
?structure (p:P703/ps:P703) ?organism.
OPTIONAL { ?structure wdt:P235 ?structure_inchikey. }
OPTIONAL { ?structure wdt:P233 ?structure_smiles. }
OPTIONAL { ?structure wdt:P231 ?structure_cas. }
OPTIONAL { ?organism wdt:P961 ?ipniID. }
SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}
LIMIT 100000
:return:

Hello,
I can see we can download certain files for the full database, but in these, I couldn't find a file that includes the source organisms.
Interesting enough (and I've being using it; thank you), I can search for genus and download a .sdf file with this information...

Thank you again for this database.

I'm trying extract all metabolites in a plant order and include given CAS ID, INCHIKey and Smiles information. When I run:

SELECT DISTINCT ?structure ?structureLabel ?structure_smiles ?structureCAS ?structureINCHIKEY ?organism ?organism_name WHERE {
  VALUES ?taxon {
    wd:Q21754                                    # You can remove the Qxxxxxx and hit Ctrl+space, type the first letters and it should autocomplete
  }
  ?organism (wdt:P171*) ?taxon;                   # Include children taxa
                        wdt:P225 ?organism_name.  # Get organism name
  ?structure wdt:P233 ?structure_smiles;          # Get the SMILES
             (p:P703/ps:P703) ?organism.          # Found in given taxon/taxa

  SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}
LIMIT 100000

I get 20968 results, however when I try to include CASID and INCHIKEY information with the following:

SELECT DISTINCT ?structure ?structureLabel ?structure_smiles ?structureCAS ?structureINCHIKEY ?organism ?organism_name WHERE {
  VALUES ?taxon {
    wd:Q21754                                    # You can remove the Qxxxxxx and hit Ctrl+space, type the first letters and it should autocomplete
  }
  ?organism (wdt:P171*) ?taxon;                   # Include children taxa
                        wdt:P225 ?organism_name.  # Get organism name
  ?structure wdt:P233 ?structure_smiles;          # Get the SMILES
             (p:P703/ps:P703) ?organism;          # Found in given taxon/taxa
             wdt:P231 ?structureCAS;          # Get the CAS
             wdt:P235 ?structureINCHIKEY.          # Get the INCHIKEY

  SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}
LIMIT 100000

I only get 7967 results. I imagine this might be because the latter query doesn't return instances without a CAS ID or INCHIKEY. Is it possible to return all metabolites found in taxa and leave missing values for the properties as NaN?

Originally posted by @alrichardbollans in #27 (comment)

I was wondering if the information on https://lotus.naturalproducts.net/download is correct, that the latest version of the database in Mongo is from Feb. 2021. I am interested to know when a new release will be available. Thanks. Stuart

In https://lotus.naturalproducts.net/compound/lotus_id/LTS0194649 LOTUS lists chloroquine as being found in Cinchona calisaya which is incorrect (the given reference doesn't say that cholorquine is present in this species). I believe this issue is also the same for Alkanna orientalis.

to clarify reusability

After going into mongo and dropping the database NPOC2021 we get the following which indicates we have no data to reinstall. How do we solve this?

> db.dropDatabase()
{ "ok" : 1 }
> exit
bye
root@54ce1f4c6c12:/mongodata# cd mongodata/NPOC2021/NPOC2021/
bash: cd: mongodata/NPOC2021/NPOC2021/: No such file or directory
root@54ce1f4c6c12:/mongodata# 

Hello,

I may have noticed some inconsistencies between the data available by SPARQL request on Wikidata and those available on the LOTUS web interface, which I understood as a mirror of what's in Wikidata.

For instance, N(6)-(1,2-dicarboxyethyl)-AMP (Q2823236) in found produced by Valsa sordida (Q7912606) and this relation is referenced by the publication Phosphoproteomic and Metabolomic Profiling Uncovers the Roles of CcPmk1 in the Pathogenicity of Cytospora chrysosperma (https://doi.org/10.1128/SPECTRUM.00176-22). However, this relation does not seems to be available on the LOTUS interface.

Is this just an update issue ?

Thanks for your help.

If you search in LOTUS for Valencene, you get two hits:
Q105219112 and
Q289496.
They look the same to the uninitiated user, at least in the hit list. Certainly, the one with stereochemistry should be displayed in the LOTUS hitlist accordingly.

The two original entries for Valencene in Wikidata (https://www.wikidata.org/wiki/Q289496 and http://www.wikidata.org/entity/Q105219112) are different. One has no stereochemistry but species annotations and the other one has stereochemistry. The two InChI keys are different. I guess they should still be merged on LOTUS.

Hi, thanks for your efforts on the valuable database.
I want to get all natural compounds found in Plantae with information of Chemical ontology, Organism taxonomy and smiles, and I tried to download data from MongDB. However I found the data is not consistent with that in the Lotus website.
For example, this is the organism source for LTS0257199 from MongoDB and website.

I wonder how I can get the source of organism with the same form as the website that I can clearly know its Phylum, Family, Genus, Species, etc. Can I get all these information by wikidata query? If so, how to use wiki query to get all compounds from Plantae?
Thanks!

See https://bioregistry.io/registry/lotus

it would be a small snippet of JSON-LD wrapped in a <script> element... the content can be autogenerated from the content on the page. I will make a template for https://lotus.naturalproducts.net/compound/lotus_id/LTS0249032 asap.

Optionally provide the original file and/or upload it to https://commons.wikimedia.org/wiki/Main_Page

@oolonek, @mSorok Your take?