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upload RIKEN_ReSpect MS2 #82

Closed zzjl20 closed 5 years ago

meier-rene commented 5 years ago

Thank you for this new contribution. Could you please give a short introduction about the source of these spectra and who contributed them. You have already contributed a number of records, some in the RIKEN directory and some in some directories which start with RIKEN and then have something like a project tag (RIKEN_IMS, RIKEN_NPDepo). For the older content of MassBank we maintain a list if contributors (https://github.com/MassBank/MassBank-data/blob/master/List_of_Contributors_Prefixes_and_Projects.md) and I would like to put some entries for your contributions in this list.

Do you want to mark these contribution with a specific poject tag and thats why you use RIKEN _ReSpect?

I would like to put this topic up for discussion to some of the senior MassBank member. How should we handle different projects coming from a certain institution? How should we handle new prefixes for accessions?

@sneumann @schymane @tsufz

zzjl20 commented 5 years ago

For the description of these RIKEN_ReSpect record: All data sorted from RIKEN Center for Sustainable Resource Science : Metabolomics Research Group. I just transform the data to MassBank format.

At this time, these data come from one institute (if you see closer into the data, you will find records from different experiment, year and authors...) So that is why I would like to request for a independent directory.

As I know, Riken have several affiliate institute. Many of them be able to carry experiments.

There should be a rule to how to handle the new prefix. Also tell the new contributor when and how to use a new prefix.

schymane commented 5 years ago

@tsufz and I will be in the same physical location for the next few days so I will put this on the list to discuss. We have had a parallel email discussion regarding new contributors as well, as well as relaxing the accession ID requirements. @meier-rene do you want to start a separate issue (or issues if needed) to discuss this in an overarching manner? We may need to cross-ref with MassBank-web. Please break issues down into topics if this is logical for you.

Re ReSpect I have some concerns as the original ReSpect dataset was imported from a fixed set that was published. http://spectra.psc.riken.jp/ It does not look like this has moved much since 2013; but it is the same group as @zzjl20 indicates. If these are new contributions that add to ReSpect, then I feel this should go into the same directory, the contribution date and other info will tell is that these are new (this is e.g. what happens with the Eawag set all the time, with new contributions).

It is plausible that other RIKEN groups will contribute too. Also note for Eawag we have mulitple letter combinations but in one directory (EA = Orbitrap and EQ = QExactive, for instance), with the tentative spectra separated out into a different directory as they were made differently (with ET or ETS prefix). We should come up with some kind of guidance.

zzjl20 commented 5 years ago

I suggest 2 ways how to use prefix:

  1. Group name_ Affiliate name. Just like I upload RIKEN_IMS, RIKEN_NPDepo... This allowed infinite affiliate institute. But maybe the management of prefix would be hard work.

  2. Prefix only allowed for certain group, for example PR is for RIKEN. Then 3rd position use A-Z to indicate different sub-institute. PRA for RIKEN_IMS, PRB for RIKEN_NPDepo .... This allowed every group maximum 26 sub-institute/lab, every lab is enable to upload 100,000 records.

This is only my suggestion only for your information.

I am dealing with a dataset from a joint research by Karolinska institute (Sweden)and Gunma University(Japan). The author requests me to use a new directory named "KI_Gumma"... What should we do with joint contributors?

Previously I upload RIKEN PlaSMA records to "RIKEN" directory (trying to reduce the number of the folder...). The author request me to separate these records from RIKEN, for PlaSMA is a group...

meier-rene commented 5 years ago

We totally understand your point here. Please give us a little bit of time to come up with a feasible solution which makes everyone happy

meier-rene commented 5 years ago

I made some research about the data you submitted and found out, that they are from independent institutions. Thats why I took over your naming scheme and I will enter some information in the table of contributors.

zzjl20 commented 5 years ago

Dear Rene Meier ,

Thank you very much for the information.

If you need any other information, please feel free to contact me.

LI

René Meier notifications@github.com 于2019年8月6日周二 下午9:04写道：

I made some research about the data you submitted and found out, that they are from independent institutions. Thats why I took over your naming scheme and I will enter some information in the table of contributors.

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