HUPO-PSI / mzTab

mzTab Reporting MS-based Proteomics and Metabolomics Results
https://hupo-psi.github.io/mzTab
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Resurrect col_unit elements, especially for optional columns #131

Closed nilshoffmann closed 6 years ago

nilshoffmann commented 6 years ago

In PR #124, colUnits were removed from the specification. However, for optional columns, there is currently no simple way to define which unit the values they report hold, if their column name is not specified via a CVParam. AFAIU, user params do not make sense for optional column names, thus, an optional column with a specified name can only have assigned units for the values it reports via the col_unit mechanism.

andrewrobertjones commented 6 years ago

So you mean have something like the following:

MTD colunit-small molecule opt_ms_run[1]_cv_MS:MS:1002476_ion_mobility_drift_time=[UO,UO:0000031, minute,]

Yes I agree that make sense. Shall I re-instate it?

nilshoffmann commented 6 years ago

Yes, please. The code is still working :-)

nilshoffmann commented 6 years ago

Or for the opt_global_mass_error column: MTD colunit-small_molecule_evidence opt_global_mass_error=[UO, UO:0000169, parts per million, ]

andrewrobertjones commented 6 years ago

Re-instated but needs a new CV term for my example to be valid, which I posted a request for

nilshoffmann commented 6 years ago

Fixed by #135