mzTab-M to MetaboLights ISA converter
Opened this issue · 3 comments
To simplify preparation of submissions to EBI MetaboLights, converting mzTab-M to MetaboLights' ISA format would be very helpful.
Where to put that ? into https://github.com/aberHRML/metabolighteR
or into https://github.com/ISA-tools/Risa/ or via the python interface
https://cran.r-project.org/web/packages/reticulate/ into https://github.com/ISA-tools/isa-api
or es export from https://github.com/lifs-tools/rmzTab-m/ ?
Yours, Steffen
@sneumann currently working on this with the MetaboLights team using Python and Pydantic binding from the JSON schema model of the format. So input will be the JSON format, which can be created using jmztab-m and / or the corresponding Docker container. Output will be MetaboLights ISA-Tab.
Super cool. We should include that into the use cases for xcms / MSIO output (https://github.com/RforMassSpectrometry/MsIO and sneumann/xcms#698 (comment)),
export from mzMine (mzmine/mzmine#1640 (comment))
and existing export from MS-Dial. I keep poking for example mzTab-M's from these implementations, and we should test-submit all example files we have here in HPU-PSI repo.
Yours, Steffen