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mwang87 / ReDU-MS2-GNPS

User interface to reanalyze and explore all public data in Metabolomics Public Data
https://redu.ucsd.edu/
MIT License
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Marine Nudibranch #203

Closed viqqikurnianda closed 4 years ago

viqqikurnianda commented 4 years ago

The content for NCBI Taxonomy

alan-jarmusch commented 4 years ago

Hi @viqqikurnianda - are you requesting that the following be added as options?Phyllidiella pustulosa Phyllidiella aff. nigra Phyllidiella krempfi Phyllidiella sp1. Phyllidiella sp2.

alan-jarmusch commented 4 years ago

@viqqikurnianda I was able to find

viqqikurnianda commented 4 years ago

Dear,

Thank you for the information.

I would like to confirm that:

1881994|Phyllidiella nigra Yes, It is refer to Phyllidiella aff. nigra.

154615|Phyllidiella Yes, I agree with you. It can be used for the species 1 and 2.

For Phyllidiella krempfi, I could not found any information. We can skip for this species.

Would you please process for (a) 154616|Phyllidiella pustulosa, (b) 1881994|Phyllidiella nigra, and (c) 154615|Phyllidiella.

Thank you for the helps.

Regards,

Viqqi

On 2 Jul 2020, at 03.13, alan-jarmusch notifications@github.com wrote:

@viqqikurnianda I was able to find

154616|Phyllidiella pustulosa 1881994|Phyllidiella nigra (Is this = to Phyllidiella aff. nigra?) I cannot find an NCBI taxonomy ID for this Phyllidiella krempfi - can you provide? If not, then we will proceed without one. 154615|Phyllidiella (this can is the NCBI taxonomy ID for the genus and can be used for your species 1 and 2) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

viqqikurnianda commented 4 years ago

Dear Mr.,

Thank you for updating the NCBI Taxonomy in ReDU. However, I could not pass the ReDU validator when I choose 154616|Phyllidiella pustulosa as the NCBI Taxonomy. Moreover, when I choose another species such as 70919|Sarcophyton glaucum, it would passed the ReDU validator.

Would you please to help me for this condition?

Also, I present the template as proof.

Regards,

Viqqi

On 2 Jul 2020, at 03.13, alan-jarmusch notifications@github.com wrote:

@viqqikurnianda https://github.com/viqqikurnianda I was able to find

154616|Phyllidiella pustulosa 1881994|Phyllidiella nigra (Is this = to Phyllidiella aff. nigra?) I cannot find an NCBI taxonomy ID for this Phyllidiella krempfi - can you provide? If not, then we will proceed without one. 154615|Phyllidiella (this can is the NCBI taxonomy ID for the genus and can be used for your species 1 and 2) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mwang87/ReDU-MS2-GNPS/pull/203#issuecomment-652571957, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP5QYND6HW3GJ5K7IIDU7WTRZN4FXANCNFSM4ONMEEXA.

alan-jarmusch commented 4 years ago

hi @viqqikurnianda, great. I have added those species to the template (as I think you have discovered). The reason that the file failed to validate - I had not pushed an update to the validator as I'm just now getting to the response. I'll submit the update now and the validator will be updated with the next release. For now, you can proceed with uploading to massive if the only errors were related to the taxonomy. If you don't see your data appear in the file selector in the next couple of days please follow up with me. I apologize for the delay in updating - things are a bit slower than normal.

viqqikurnianda commented 4 years ago

Dear Mr.,

Thank you for the email.

It work.

Thank you for the helps.

Regards,

Viqqi

On 3 Jul 2020, at 08.59, Ming Wang notifications@github.com wrote:

Closed #203 https://github.com/mwang87/ReDU-MS2-GNPS/pull/203.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/mwang87/ReDU-MS2-GNPS/pull/203#event-3509095956, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP5QYNH3Y7TBCMNBGIKLYG3RZUNPRANCNFSM4ONMEEXA.