Classyfire information could be pulled from SMILES

[mabelgon88]

Is your feature request related to a problem? Please describe. For most of the compounds found in poison frogs I have felt frustrated because the Classyfire informartion is not available almost never. When I look manually inside classyfire with SMILES (not InChI) I have found the taxonomy related with many of these compounds actually exist, so I suspect that GNPS is taking InChIKey for filling these fields in GNPS, but not SMILES, probably because some of the are not reported on libraries.

Describe the solution you'd like I would like to have the classyfire taxonomy available inside GNPS and I think that if the search is based on SMILES this is going to be possible. I suspect that there are more compounds with SMILES and not InChIKey, so probably this addition would be also useful for many users that analyze not very common compounds. The problem here is that maybe de library does not report the SMILES, so what I did was looking the InChIKey in Pubchem, and then copying the SMILES into Classyfire.

Additional context Here is an example of some indolizidines found in this dataset. https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D you can see that classyfire taxonomy is not visible, but using the first compound I show you here an example of the taxonomy available in Classyfire: http://classyfire.wishartlab.com/entities/ONNRIWKYSUKBOB-UHFFFAOYSA-N

[mwang87]

In inspecting the link provided, the vast majority of the indolizidine molecules do not have any structure associated with them in the library. Without structure it is not possible to classify them.

[mabelgon88]

Hi Ming. Many of the listed structures are isomers of the first one, which is probably the most likely correct annotation. So, my question is related specifically with the first match of the list (not all matches), because in that case we have a structure, but I think that the problem is that as these compounds were included in the older version of NIST where the authors didn't include the SMILES or InChIKey, but both of them are now (2020) available in PubChem. There is some query that we can use for adding that information into the libraries, or if I do it manually for many of them do you think that we can include it as a personal open library of alkaloids from amphibians? or what do you suggest?

[mabelgon88]

Here is an example of the information from this first match. https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572476#%7B%7D in this case it's the opposite, the SMILES is not available, but the InChIKey is available

[mabelgon88]

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

[mwang87]

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez notifications@github.com wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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[mabelgon88]

Hi,

For example this one: https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7Dhttps://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}

Name: (5Z,9E)-5-Propyl-3-butylindolizidine InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang notifications@github.com<mailto:notifications@github.com> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

[mwang87]

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez notifications@github.com wrote:

Hi,

For example this one: https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D < https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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[mabelgon88]

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang notifications@github.com<mailto:notifications@github.com> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com> wrote:

Hi,

For example this one: https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D < https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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.

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

[mwang87]

Where is it missing? can you link and provide a screen shot?

On Tue, Nov 17, 2020 at 2:46 PM Mabel Gonzalez notifications@github.com wrote:

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com>> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com> wrote:

Hi,

For example this one:

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D <

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine

InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang <notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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[mabelgon88]

It’s the third entry here:

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

GNPS Library Spectrum CCMSLIB00002572470

On Nov 17, 2020, at 5:57 PM, Ming Wang notifications@github.com<mailto:notifications@github.com> wrote:

Where is it missing? can you link and provide a screen shot?

On Tue, Nov 17, 2020 at 2:46 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com> wrote:

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi,

For example this one:

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D <

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine

InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.commailto:notifications@github.com>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

[mwang87]

I think the email is not showing anything. All I see if

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

On Tue, Nov 17, 2020 at 3:10 PM Mabel Gonzalez notifications@github.com wrote:

It’s the third entry here:

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

GNPS Library Spectrum CCMSLIB00002572470

On Nov 17, 2020, at 5:57 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com>> wrote:

Where is it missing? can you link and provide a screen shot?

On Tue, Nov 17, 2020 at 2:46 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com><mailto: notifications@github.commailto:notifications@github.com>> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi,

For example this one:

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D

<

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine

InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang <notifications@github.com mailto:notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com<mailto: notifications@github.com>>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez < notifications@github.commailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

— You are receiving this because you commented.

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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[mabelgon88]

I don’t know what’s going on with the attachment. Can you see it now?

[cid:9A5A1AF6-2990-4644-BC6D-EF7AB9134CEB@ucsd.edu]

On Nov 17, 2020, at 6:19 PM, Ming Wang notifications@github.com<mailto:notifications@github.com> wrote:

I think the email is not showing anything. All I see if

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

On Tue, Nov 17, 2020 at 3:10 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com> wrote:

It’s the third entry here:

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

GNPS Library Spectrum CCMSLIB00002572470

On Nov 17, 2020, at 5:57 PM, Ming Wang notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> wrote:

Where is it missing? can you link and provide a screen shot?

On Tue, Nov 17, 2020 at 2:46 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com><mailto: notifications@github.commailto:notifications@github.commailto:notifications@github.com>> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi,

For example this one:

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D

<

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine

InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang notifications@github.com<mailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.commailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez < notifications@github.commailto:notifications@github.commailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

[mwang87]

I don't see an attachment. Perhaps use the github interface rather than email.

On Tue, Nov 17, 2020 at 3:33 PM Mabel Gonzalez notifications@github.com wrote:

I don’t know what’s going on with the attachment. Can you see it now?

[cid:9A5A1AF6-2990-4644-BC6D-EF7AB9134CEB@ucsd.edu]

On Nov 17, 2020, at 6:19 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com>> wrote:

I think the email is not showing anything. All I see if

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

On Tue, Nov 17, 2020 at 3:10 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com> wrote:

It’s the third entry here:

[cid:77E2E079-E46E-4D89-9370-33410DF54F29@ucsd.edu]

GNPS Library Spectrum CCMSLIB00002572470

On Nov 17, 2020, at 5:57 PM, Ming Wang <notifications@github.com<mailto: notifications@github.com><mailto: notifications@github.commailto:notifications@github.com>> wrote:

Where is it missing? can you link and provide a screen shot?

On Tue, Nov 17, 2020 at 2:46 PM Mabel Gonzalez <notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming,

I’m sorry but I’m think I am not following you. That’s means that the taxonomy should be available? It is possible that the taxonomy is not visible in GNPS, but it’s visible in the .csv file output from the library search? Because here says none, none, none. That example it’s the third compound.

[cid:D3B76BE7-6F16-49E9-A1A6-E30BE19AD272@ucsd.edu]

On Nov 17, 2020, at 5:41 PM, Ming Wang <notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com><mailto: notifications@github.commailto:notifications@github.com<mailto: notifications@github.com>>> wrote:

This one is already classified in our cache so it should not be a problem:

https://gnps-structure.ucsd.edu/classyfire?inchi=InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

Ming

On Tue, Nov 17, 2020 at 2:39 PM Mabel Gonzalez < notifications@github.commailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi,

For example this one:

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D

<

https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#{}>

Name: (5Z,9E)-5-Propyl-3-butylindolizidine

InChI=1S/C15H29N/c1-3-5-8-14-11-12-15-10-6-9-13(7-4-2)16(14)15/h13-15H,3-12H2,1-2H3

When I look that InChI in Classyfire I found this: http://classyfire.wishartlab.com/queries/5336187

Thanks a lot Ming. I hope that you can help me.

On Nov 16, 2020, at 11:36 PM, Ming Wang <notifications@github.com mailto:notifications@github.com mailto:notifications@github.com mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com<mailto: notifications@github.com><mailto: notifications@github.commailto:notifications@github.com>>> wrote:

Can you list a single entry that you think should be classified?

On Mon, Nov 16, 2020 at 8:33 PM Mabel Gonzalez < notifications@github.commailto:notifications@github.com<mailto: notifications@github.com> mailto:notifications@github.com mailto:notifications@github.com> wrote:

Hi Ming!

I just cloned that job as you told me and still, the taxonomy is not available for these compounds.

This is the new job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

And this is the old job:

https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=2f4aacd2edf0461aa327aa577c553c5d&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

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Best regards,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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Best regards / Cordialmente,

Mabel Cristina González Montoya, M.Sc. Ph.D. Student Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP) Chemistry Department Universidad de los Andes Carrera 1 #18A-10, Bogota, Colombia

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[mabelgon88]

[mabelgon88]

Hi Ming! I sent the attachment trough GitHub. Can you see it now?

Best regards / Cordialmente,

[mwang87]

Which link goes with the image, I can see the image now. Also can you not respond via email, or if you do, remove the tail of the email. its a bit unreadable now.

[mabelgon88]

I'm so sorry Ming. I haven`t seen all the long tail.

This is the link of the indolizidines for the screenshot: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

This is the link of the compound: https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00002572470#%7B%7D

And I've attached the image again:

[mabelgon88]

Hi Ming! Happy holidays for you and your family! I wanted to ask you if do you have any updates about this request. thanks

[mabelgon88]

Hi Ming!

I´ve checked the old file more than 2 months later and I still didn't find the classyfire taxonomy populated from the amphibian alkaloids such as indolizidines. Do you know another fast way how I can populate this information, maybe by my own, outside GNPS?

This is an example of none classification for indolizidines of that last job I re-runed in november. https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=f09b861a4d044e6d9a5bcf6a9b022664&view=view_all_annotations_DB&show=true#%7B%22main.Compound_Name_input%22%3A%22indolizidine%22%7D

[mwang87]

Thanks for letting us know, we haven't pushed an update for this in a while.

If you want to do it outside, you could write some code to hit the api end points to get the data you need. I think you have so many, automation is the best.