Added format mzTab-M

[cb2993]

Hi,
With @sneumann we have gone through some data formats in chemistry and want to add the format mzTab-m from @HUPO-PSI.

A issue #784 has already been created and herewith the corresponding PR shall be submitted.

I hope it is correct, this one is my first PR @matuskalas .
Yours, Claudia.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[matuskalas]

Thank you so much Claudia for your pull request, and a warm welcome among the EDAM contributors! 😊🙌🏽
Honestly, this is the absolutely cleanest first-time contribution in the history of EDAM 🥇 Highly appreciated! 🙏🏽

TODO: I'll merge it asap, and at the same time I'll assign it the ID and check all the links. So as far as I can see, the only TODO is on me. 😉 But I'll ask in case anything turns out unclear. Maybe 1 immediate question to double-check the compatibility: Is any valid mzTab-M-formatted data also valid as mzTab?

I hope you'll have a chance to contribute more in the future! 🦑 Please feel free to ask if you have any questions related to that.
You're also welcome to join the EDAM community chat, which at the very moment has zero traffic, but that should change in the future 😄 You're super welcome to ask any public questions there, anytime! This all applies to you @sneumann too!😊

We would love to add you onto the list of co-authors @cb2993, so if you don't mind being listed, please send me your author details (especially name). You're very welcome to do that privately using my university email, and we will NOT publicly associate your personal info with your GitHub account. Any privacy concerns are welcome👍🏽

Many thanks again,
Matus

[sneumann]

HI @matuskalas,
no, after mzTab (1.0) the mzTab-M 2.0 has diverged, and is not compatible anymore. General concepts remain, but parsers (beyond set of CSVs) will not be compatible. And yes, happy to be listed as contributor. Yours, STeffen

[matuskalas]

This is awesome👍🏽 we can merge it and fix the ID (rdf:about..) right before the merge

[LucieLamothe]

Hi @cb2993 @sneumann, when you say that the two format are not compatible what do you mean exactly? For example the tools are they able to read both file? Is the conversion from one the the other is easily doable? I'm asking this so we can determine whether to have mzTab-M as subclass of the existing format mzTab or as "brother" of mzTab (both subclass of Mass spectrometry data format).

Thank you so much for yor help :)

Lucie L

[sneumann]

Hm, @nilshoffmann might be able to chime in. MzTab 1.0 and the mzTab-* 2.0 formats will both be readable by CSV readers ;-) Both have a Metadata section that should be compatible. Readers for 1.0 will choke (or ignore) on the actual data in mzTab-M 2.0. It is not likely that a reader for 2.0 faithfully consumes 1.0 files. I would expect that a software would have two readers, and detect file version to decide which reader to call.
Was that helpful ? Yours, Steffen
P.S.: Technically I'd say mzTab-M should be a sibling to mzTab-1.0 , historically it'd be a child.

[nilshoffmann]

@LucieLamothe @sneumann The mzTab-M format comes with separate parser and validator implementations. Generic CSV readers may read both formats, but the metadata sections and specifically the content sections are not compatible, although they share some structure. Conversion from mzTab to mzTab-M would be possible, but only on summary level. The other way around may be possible, but only with loss of information. I would therefor also see mzTab-M more as a sibling and "brother in spirit".

[matuskalas]

Thanks a lot for the clarifications @sneumann & @nilshoffmann 🙏🏽

[matuskalas]

Million thanks indeed 🙇🏽‍♂️ I think this is rather clear now.

One note from the live chat: Just like ISA-TAB, mzTab-M can use any ontologies inside. PSI-MS is the main and most obvious, and some other main ones are listed in https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_2_0-M_mapping.xml. However, any other can be used, too.

[nilshoffmann]

@matuskalas Is there anything that we need to change / update to get this PR merged?

[nilshoffmann]

Pinging @matuskalas to kindly ask to proceed with the merging of mzTab-M

[nilshoffmann]

And pinging @matuskalas again to kindly ask to proceed with the merging of mzTab-M. Not sure why the CI build failed, the logs are no longer available.

[hechth]

@matuskalas I'd also like to ask if this could be added? Would be great! Thanks!

[nilshoffmann]

@matuskalas @LucieLamothe What is the status of this PR? Is there a timeline when it might be merged?

[LucieLamothe]

I left this project last year I'm sorry I won't be able to help :/