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Why are the metadata options exclusive?

See original GitHub issue

Hi,

I have a question regarding the -m, --metadata=VALUE option. The possible values are 0 for JSON, 1 for TXT. However upon inspection it is clear the json and txt selections are not format output choices, because the files have different contents with only small overlaps.

Why is this the case? In our use case we want to preserve all the metadata - the info in json for public repository deposition and the info in txt for downstream analysis steps.

Is it realistic to rerun the parser on the same input to gain both of these metadata files? Is there a better option?

Issue Analytics

State:
Created 3 years ago
Comments:8 (3 by maintainers)

Top GitHub Comments

1reaction

nielshulstaertcommented, Apr 1, 2021

JSON and TEXT output formats output the same metadata fields in release 1.3.3

1reaction

nielshulstaertcommented, Mar 29, 2021

Hi @edeutsch , @ypriverol , @martenson ,

This table shows the metadata entries for both JSON and TEXT formats I would like to add in the next release. This way, both formats contain the same data and it should be backwards compatible. I tried to find appropriate CV terms for all of the fields, let me know if this looks good or if you have other suggestions.

JSON	TXT	Empty check
FileProperties
Pathname (NCIT:C47922)	RAW file path
Version (NCIT:C25714)	RAW file version
Content Creation Date (NCIT:C69199)	Creation date
Description (NCIT:C25365)	Description	x
InstrumentProperties
Thermo Scientific instrument model (MS:1000494)	Instrument model
instrument attribute (MS:1000496)	Instrument name
instrument serial number (MS:1000529)	Instrument serial number
Software Version (NCIT:C111093)	Software version
firmware version (AFR:0001259)	Firmware version	x
MsData
Number of MS1 spectra (PRIDE:0000481)	Number of MS1 spectra
Number of MS2 spectra (PRIDE:0000482)	Number of MS2 spectra
Number of MS3 spectra (PRIDE:0000483)	Number of MS3 spectra
MS min charge (PRIDE:0000472)	MS min charge
MS max charge (PRIDE:0000473)	MS max charge
MS min RT (PRIDE:0000474)	MS min RT
MS max RT (PRIDE:0000475)	MS max RT
MS min MZ (PRIDE:0000476)	MS min MZ
MS max MZ (PRIDE:0000477)	MS max MZ
ScanSettings
scan start time (MS:1000016)	Scan start time
mass resolution (MS:1000011)	Mass resolution
mass unit (UO:0000002)	Units
Number of scans (PRIDE:0000478)	Number of scans
MS scan range (PRIDE:0000479)	Scan range
Retention time range (PRIDE:0000484)	Time range
Mz range (PRIDE:0000485)	Mass range
fragmentationType	Fragmentation types
SampleData
sample name (MS:1000002)	sample name	x
sample number (MS:1000001)	sample ID	x
type (NCIT:C25284)	sample type	x
Comment (NCIT:C25393)	sample comment	x
Vial (NCIT:C41275)	sample vial	x
sample volume (MS:1000005)	sample volume	x
injection volume setting (AFR:0001577)	sample injection volume	x
Row (NCIT:C43378)	sample row number	x
dilution factor (AFQ:0000178)	sample dilution factor	x

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