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Update records to be compliant with Record Format 2.4 #99

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tsufz opened this issue Oct 31, 2019 · 3 comments
Open

Update records to be compliant with Record Format 2.4 #99

tsufz opened this issue Oct 31, 2019 · 3 comments
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compliance with Record Format Issues for data curation based on Record Format data curation This issue is related to data curation. feature for validation

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@tsufz
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tsufz commented Oct 31, 2019

The following fields and entries do not comply to the latest Record Format and should be changed in the data for harmonisation.

Those tags are wrongly used or the terms changed during the last years:

AC$MASS_SPECTROMETRY: FRAGMENTATION_METHOD -> AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE

AC$MASS_SPECTROMETRY: FRAGMENT_VOLTAGE -> AC$MASS_SPECTROMETRY: IONIZATION_ENERGY

AC$MASS_SPECTROMETRY: IONIZATION_POTENTIAL -> AC$MASS_SPECTROMETRY: IONIZATION_ENERGY

AC$MASS_SPECTROMETRY: RESOLUTION_SETTING -> AC$MASS_SPECTROMETRY: RESOLUTION

AC$MASS_SPECTROMETRY: ION_SOURCE_TEMPERATURE -> AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE

AC$CHROMATOGRAPHY: CAPILLARY_VOLTAGE -> AC$MASS_SPECTROMETRY: CAPILLARY_VOLTAGE

AC$CHROMATOGRAPHY: INJECTION_TEMPERATURE -> AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE

AC$CHROMATOGRAPHY: RETENTION_INDEX -> AC$CHROMATOGRAPHY: KOVATS_RTI
I checked all entries, they are in the 1000er ranges and thus it is very propably that they are related to the KOVATS_RTI

AC$CHROMATOGRAPHY: OVEN_TEMPERATURE -> AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE_GRADIENT

MS$FOCUSED_ION: PRECURSOR_M/Z -> MS$FOCUSED_ION: PRECURSOR_MZ
@meowcat mentioned that we should avoid slashes in the tags.

This is just a typo:
AC$CHROMATOGRAPHY: TRANSFARLINE_TEMPERATURE -> AC$CHROMATOGRAPHY: TRANSFERLINE_TEMPERATURE

The following tags can be merged into AC$MASS_SPECTROMETRY: MASS_RANGE_MZ
AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z
AC$MASS_SPECTROMETRY: SCAN_RANGE_M/Z
AC$MASS_SPECTROMETRY: SCANNING_RANGE

@tsufz tsufz added data curation This issue is related to data curation. feature for validation compliance with Record Format Issues for data curation based on Record Format labels Oct 31, 2019
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tsufz commented Oct 31, 2019

I forgot the scanning issue MassBank/MassBank-web#200:

AC$CHROMATOGRAPHY: SCANNING -> AC$CHROMATOGRAPHY: SCANNING_SETTING

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tsufz commented Dec 4, 2019

@meier-rene Do you have Any plan about this issue?

@tsufz tsufz closed this as completed Dec 4, 2019
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tsufz commented Dec 16, 2019

Was closed on chance...

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compliance with Record Format Issues for data curation based on Record Format data curation This issue is related to data curation. feature for validation
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