No matches in the Molnetenhancer

[Stella Yang]

Hi everyone, we faced some issues last few weeks when we used some annotated tools like Molnetenhancer. We used data that worked well before, and all codes displayed same color and described no matches. Can you please help me deal with that issues?

Kind regards,

Stella Yang

[TonioG]

I have been experiencing the same issue at the end of july just before going on holidays. Even with previous results which had worked fine didn't work anymore, not a single match.

Don't know if it has been addressed yet, any news?

Antonio

[Daniel Méndez Rodríguez]

I have the same problem. Not a single match, doesn't matter what parameters I select. I hope it can be solved soon.

Regards, Daniel

[TonioG]

Don't for you guys but on my side, MolNetEnhancer is still ko.

Antonio

[Daniel Méndez Rodríguez]

The same goes for me. It's still not working.

Daniel

[Daniel Quiroz Moreno]

The same goes for me,

I have a MolNetEhnahcer task that worked before, I cloned and relaunched the same tasks, and same IDs, and it´s not working.

Daniel

[Ainsely Lewis]

Hello everyone!

How are you? I hope you are well.  I have the same issue. We have a paper due soon for revisions (9 days time) and no clue what is going on.  This data is needed for us. 

Workflow for now is using Classical Molecular Networking. Used dereplicator+, MS2LDA, and NAP in MolNetEnhancer. Still nothing regarding metabolite classes in Cytoscape.  

Deleting jobs prior as FBMN was not really working annotation-wise using dereplicator+, MS2LDA, and NAP. 

Am I doing something wrong? 

Thank you. 

[Yanick Kevin Melogmo]

Greeting to all,

I have the same problem.

Not matching in the MolNetEnhancer.

Someone can help to fix the problem? Please


Thank you

Yanick Melogmo, MSc
PhD student, Biochemistry
Antimicrobial and Biocontrol Agent Unit
Tel: +237 678 900 517 / 693 319 236
Email: melogm...@gmail.com / y.me...@s2-gmbh.com
Skype: Yanick_Melogmo

-------- Original Message --------
Subject: [GNPS Forum] Re: No matches in the Molnetenhancer
From: Ainsely Lewis
To: GNPS Discussion Forum and Bug Reports
CC:

Hello everyone!

How are you? I hope you are well.  I have the same issue. We have a paper due soon for revisions (9 days time) and no clue what is going on.  This data is needed for us. 

Workflow for now is using Classical Molecular Networking. Used dereplicator+, MS2LDA, and NAP. Still nothing regarding metabolite classes in Cytoscape.  

Deleting jobs prior as FBMN was not really working annotation-wise using dereplicator+, MS2LDA, and NAP. 

Am I doing something wrong? 

Thank you. 

On Wednesday, September 6, 2023 at 11:14:03 AM UTC-4 Daniel Quiroz Moreno wrote:

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[Ainsely Lewis]

Hello. So I am getting an error message accessing GNPS. 

It seems like they are working on the issue. 

Attached is a screenshot. 

[soliman khatib]

Hello,

  , I also face the same problem, all the nodes show no match with the same color 
 
Any help to solve the problem?

Thanks,
Soliman

ב-יום חמישי, 7 בספטמבר 2023 בשעה 22:41:23 UTC+3, Ainsely Lewis כתב/ה:

[שחף רופא‎]

Hello eveyone,

It seems the problem still exist. Im dealing with the same issue right now. they all displayed in the same color.
there's any clue how to solve it?

Thank you.

Shachaf

ב-יום שני, 11 בספטמבר 2023 בשעה 00:45:34 UTC+3, soliman khatib כתב/ה:

[Justin van der Hooft]

Hello all,

Thanks for brining this up. As you may know, the GNPS team is building a new GNPS infrastructure at GNPS2.org - this means that one by one, workflows will be transferred to there. In the meantime, GNPS1 will remain up, but no longer at its full capacity. Whilst we recognise that MolNetEnhancer is widely used throughout the community, it is also a tool that combines several workflows and then outputs them jointly in the graphml file. Actually, the individual components that contribute to MolNetEnhancer still seem to work - so if you are in need of the results, you could use the available workflows in R or Python from https://github.com/madeleineernst where you can run the tool and get the necessary files out to enhance the molecular network in CytoScape (as also described in the original paper).

In the coming time, the GNPS team is planning to make MolNetEnhancer also available form GNPS2.org, but we ask your patience as this involves several steps and checks to make sure that the tool is future proof.

Kind regards, on behalf of the GNPS team,

Madeleine, Justin, Alberto, Ming

[Andrea Gentile]

Dear Justin,

I am using the python MolNetEnhancer script from https://github.com/madeleineernst, but the example notebooks are not working, not even on the example data. Specifically, the cell with the code  "out = unique_smiles(matches)" always produces errors. I have posted the issue on GitHub: https://github.com/madeleineernst/pyMolNetEnhancer/issues/5

Do you have any suggestions?

Also,  I figured out that the reason why MolNetEnhancer does not produce matches is because the ClassyFire servers contacted by the tool are down:

http://classyfire.wishartlab.com

https://gnps-classyfire.ucsd.edu

I tried to get in contact and expose the problem also on GitHub but I did not get any reply so far.

Any suggestions?

Thanks,

Andrea Gentile

Naicons Srl

[Justin van der Hooft]

Good evening Andrea, all,

Thanks for your (continued) interest in the MolNetEnhancer workflow. It looks like many of you are especially interested in the chemical compound classification part of the workflow, and indeed, this part is currently not functional. The reason is that external sites do not return any classification terms for the candidate structures that are present in the molecular network - this results in the "no matches" error. Such external dependencies are one of the risks of integrative tools such as MolNetEnhancer. You could inform with the ClassyFire team if they are planning to create a new API that returns precomputed classification terms for SMILES.

On the short term, there will be no replacement for the existing workflow; however, I hope that in due time we will be able to do so through alternative means.

In the mean time, you could set up your own database with precomputed annotated structures to retrieve the classifications from (and feed into MolNetEnhancer), or rely on tools such as CANOPUS to do the chemical compound classification.

If the chemical compound classification part of the MolNetEnhancer workflow gets updated, we will let the community know.

Best,

Justin 

PS if you find a solution or set up your own classification term API, please do inform the community!

[Justin van der Hooft]

Good evening Andrea, all,

Thanks for your (continued) interest in the MolNetEnhancer workflow. It looks like many of you are especially interested in the chemical compound classification part of the workflow, and indeed, this part is currently not functional. The reason is that external sites do not return any classification terms for the candidate structures that are present in the molecular network - this results in the "no matches" error. Such external dependencies are one of the risks of integrative tools such as MolNetEnhancer. You could inform with the ClassyFire team if they are planning to create a new API that returns precomputed classification terms for SMILES.

On the short term, there will be no replacement for the existing workflow; however, I hope that in due time we will be able to do so through alternative means.

In the mean time, you could set up your own database with precomputed annotated structures to retrieve the classifications from (and feed into MolNetEnhancer), or rely on tools such as CANOPUS to do the chemical compound classification.

If the chemical compound classification part of the MolNetEnhancer workflow gets updated, we will let the community know.

Best,

Justin 

PS if you find a solution or set up your own classification term API, please do inform the community!  :-)

On Tuesday 9 January 2024 at 12:07:16 UTC+1 Andrea Gentile wrote:

[손주완/약학과]

Hello, I'm still have this issue. As you said, there is no way to solve it now? I really need this program.

Thank you.

2024년 1월 13일 토요일 오전 5시 5분 15초 UTC+9에 Justin van der Hooft님이 작성:

[Allyson McAtamney]

Hello,

I am also wondering if there is an update on this? Has anyone gotten this workflow to function successfully either on the GNPS web platform or on R/python?

Thanks in advance,

Allyson McAtamney (she/they)

Sanchez Lab

University of California, Santa Cruz