SML best_id_confidence_measure (spec doc 6.3.12)

[andrewrobertjones]

Relatively minor issue but seems possibly worth fixing, at least while the specs are under review. We are asking file producers to repeat a score type in this column of the SML table, yet they are also reported in the MTD section. It would seem better if we have just use integer codes to reference back to the measure used.

`

MTD	id_confidence_measure[1]	[MS,MS:1002889,Progenesis MetaScope Score,]
MTD	id_confidence_measure[2]	[,,Fragmentation Score,]
MTD	id_confidence_measure[3]	[,,Isotopic fit Score,]
`
...

`
best_id_confidence_measure

[MS,MS:1002889,Progenesis MetaScope Score,]
[MS,MS:1002889,Progenesis MetaScope Score,]
[MS,MS:1002889,Progenesis MetaScope Score,]
[MS,MS:1002889,Progenesis MetaScope Score,]
`

Proposed model:

`
best_id_confidence_measure

1
1
1
1
`

[kayrein]

Implementation in PR HUPO-PSI/mzTab#168

[nilshoffmann]

@andrewrobertjones I would put this up for debate whether we want to fix this right now. The spec doc still has the CvParam version inside, the implementation following this "verbose" mode. Can we live with this for now and maybe want to revise this for 2.x? And the current example files all follow this old mode (minus the MTBLS263 one that I corrected in PR HUPO-PSI/mzTab#170 )

[philouail]

I know this is an old issue, but please go through the different steps of the template below, to make it easy for us to understand what to do next with this:

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• Provide a pull request (Please add the link)
• Schema: Update mzTab_m_openapi.yml (View File)
• Specification: Update mzTab_format_specification_2_1-M.adoc with an example (View File)
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Next Steps, once we reach an agreement on the changes above:

• Create a downstream issue in the jmzTab-m repo (https://github.com/lifs-tools/jmzTab-m/issues)
• Implement and test changes in jmzTab-M
• Implement changes in R & Python implementations