Add checks for subsets

[matuskalas]

This has to be first cleaned-up in EDAM itself, see edamontology/edamontology#418

• Every data_|format_|operation_|topic_ concept has data|format|operation|topic subset
• Everything in the mainline EDAM needs subset bio
• Subsets are encoded in a desired way, ideally (Semantic) Web-friendly. Needs some more experiments first...

[joncison]

@matuskalas this check is good, but just to clarify, are you suggesting we refactor the current edam subset to bio ?

I'm not sure it's worth doing that considering downstream applications might need to be changed. But if you really think it's needed pls. post issues to both the docs and main trackers so we can update in both places. Thanks!

[matuskalas]

Yes, that's what I'm suggesting.

I'd be very surprised if that would affect the downstream applications, but we'll see.

Yes indeed, when this will be worked on in the (near or medium) future, we need to change it everywhere. EDAM: edamontology/edamontology#418 Docs: edamontology/edamontologyDocs#28

[joncison]

An additional check is that a concept has only one of topics, operations, formats or data defined.

[joncison]

QC check done, see https://github.com/edamontology/edamverify/blob/master/queries/subsetMisuse.ipynb

but the check (for now) assumes edam and not bio subset (i.e. current not desired future state). Easy enough to change for this, though.

some feedback on the code appreciated @hmenager and @albangaignard