W4M as new software term about psi-ms-cv

[chambm]

I like Galaxy as a platform and have developed tool wrappers and containerized analysis flavors for it, but it seems odd to me to classify it as any of those software types. To me it is a dataset and scientific workflow management system. It runs tools which are those software types (except acquisition software, I've never heard of an instrument acquiring data with Galaxy?).

It would the same as classifying snakemake, cromwell, KNIME, or one of many other workflow management systems as those software types.

How would you use the term?

[fgiacomoni]

Hi Matt,
W4M is galaxy based but fully dedicated to metabolomics data analysis. Strictly, you're right when you said it is not a software. Galaxy is a workflow manager and W4M is a workflow manager for metabolomics with tools for small molecule and lipids analysis and covering all treatment steps (preprocessing, stats, annotation, post processing...). I'm agree with you to remove MS:1001455.
We would like to use this term as metadata to characterize metabolomics raw datasets in our information system and in spectral MZML export from PeakForest database.

Thank you for your review.

[chambm]

I think you should use the individual tools' terms in the mzML, not the workflow system's. For example, there are quite a few pipelines that convert vendor data to mzML with msconvert; it is msconvert doing the processing, not the pipeline software, so msconvert puts the ProteoWizard software CV term in there for the "Conversion to mzML" dataProcessing step (pwiz being the name of the overall project msconvert belongs to). So I suggest whatever Galaxy tool you are running that creates the mzML, it should put its own software term in there for the "Conversion to mzML" dataProcessing step.

Note that I'm not saying custom flavors of Galaxy like W4M are not cite-worthy. Just that mzML doesn't have (or IMO need) the structure to reference which pipeline called the tool that actually created an mzML.

[fgiacomoni]

Ok Matt, I understand your point of view and finally may be it was not a good idea to submit W4M as term. Thank you for your review. A last question: do you have connection with the EDAM ontology?

[edeutsch]

Thank you for the discussion. @fgiacomoni are you content to close this issue then?