Upate of MassBank Record format for GC-data

MassBank / MassBank-web

The web server application and directly connected components for a MassBank web server

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Upate of MassBank Record format for GC-data #200

Open tsufz opened 5 years ago

tsufz commented 5 years ago

I was checking the record format in the last days. I am quite unhappy with the presentation of the scanning/ mass range section. As usual, there is very differnent data:

MASS_RANGE_M/Z 100-2000
SCANNING_RANGE 50.00-400.00
SCANNING_RANGE 211.11@hcd22.00 [50.00-220.00]
SCANNING_RANGE [50.00-390.00]
SCANNING_RANGE 100-3000
SCAN_RANGE_M/Z 85-500
SCANNING 1 amu/sec (m/z = 20-2040)
SCANNING 1 sec/scan (m/z=100-1000)
SCANNING 1.0 sec/scan (m/z = 50-1000)
SCANNING_CYCLE 1.5 cycle/sec
SCANNING 0.1 sec/scan
SCANNING 5 Sec

The scan range was identified as important by @sneumann some while ago, if I remember correctly.

However, the representation in MassBank is not consolidated.

Therefore, I suggest to restructure the scanning sector:

SCANNING MASS_RANGE_M/Z
SCANNING SCAN_CYCLE

tsufz commented 5 years ago

@schymane @sneumann @meier-rene, any comments? We promised to implement GC-HRMS in Norman and thus I would like to finalise the Records Format soon such that Nikiforos and Nikos could go ahead with the processing of records.

schymane commented 5 years ago

I would prefer MASS_RANGE_M/Z (without SCANNING in front) and maybe SCANNING_RATE or SCANNING_SETTING? They do not all appear to be cycles, there are different units relative to other units depending on the instrument (and I guess this cannot be unified easily) but SCANNING is rather unspecific.

tsufz commented 5 years ago

Well, I agree with @schymane. It's already implemented. Just tidy up and then I will upload to my fotk for comment's.

meowcat commented 5 years ago

MASS_RANGE_M/Z

Please no slashes in the entry names if we can avoid it at all...

tsufz commented 5 years ago

I agree with @meowcat.

tsufz commented 5 years ago

I pushed the updated format to https://github.com/tsufz/MassBank-web/tree/update_record_format.

Comments are welcome!

@meier-rene, I will add a specific topic for required changes in the records for the compliance with the record format in order to consolidate and curate the record meta data.

tsufz commented 5 years ago

@meocat and @schymane, just comment here and I will add the changes. I stopped the pull request.

tsufz commented 5 years ago

@schymane added the following to the closed pull requst #203:

I received an email earlier today with additional field suggestions. They want to add precursor intensity and concentration of the chemical. Do you want to hold off with revising until they have replied? For the record I suggested AC$CONCENTRATION and MS$FOCUSED_ION: PRECURSOR_INT. I mentioned we were revising it like right now ...