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bio-tools / biotoolsSchema

biotoolsSchema : Tool description data model for computational tools in life sciences
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change (or add to) the representation of galaxy services as relations between entries #188

Open hmenager opened 4 years ago

hmenager commented 4 years ago

Once again this comes from the discussion of https://bio.tools/workflow4metabolomics with @lecorguille and @joncison. Currently there is a link type of "galaxyService" for bio.tools entries, but this link does not enable cross-entry semantics such as specifying that a Galaxy instance deploys a tool, or that a tool is deployedBy a Galaxy instance. In the case of Workflow4Metabolomics, we therefore used uses and usedBy relations instead. Could we add deploys and deployedBy relations? cc @hansioan

matuskalas commented 4 years ago

This is back-and-forth AGAAAIN ......

Of course we need it. We always needed it. Many of us always knew we needed it.

And we need it a bit more generic, also for tools that provide access to other tools via web APIs, e.g. data sources in Galaxy, or external Web services in Jalview, thus deploys is too restricted.

We've many times agreed on something like provides(AccessTo), whatever we called it, and the corresponding inverse. And they were afterwards always removed by ad hoc project management decisions. Could we please stop wasting the bulk of the project time on such back-and-forth changes?

Btw., whenever we introduce it yet again, it will mean I have to redo my onerous curation from the beginning of January 2020, and all further curation I'll do in the next weeks & months. It's all about Galaxy and Debian tools.

hansioan commented 4 years ago

If there are uses cases supporting this, I am all open to have it. My only request is to carefully consider what to add (I prefer additions to changing things) so that we don't come back in 6 months and remove/change it back.

joncison commented 4 years ago

So this is what we have currently, which was intended to be general / a foundation:

Let's please @hmenager @matuskalas @hansioan agree on a revision - which (retains but) extends the above. And try to be very conservative - include only things we're certain about . Bear in mind it's a de facto mini-ontology represented as a flat enum, so the semantics need to be precise, to avoid confusion / misuse.

To me, deploys sounds like a specialism of includes and provides sounds very much like uses as defined.

Please suggest some possibilities with definitions below.

joncison commented 4 years ago

PS. see also these old threads (https://github.com/bio-tools/biotoolsSchema/issues/107 and https://github.com/bio-tools/biotoolsSchema/issues/106) which include some of your older notes on this subject @matuskalas

joncison commented 4 years ago

Hi @matuskalas @hmenager Me and @hansioan will begin work on schema-related things, so if you have some concrete proposals (beyond what was already said above) pls. let us know here so we can consider it for next biotoolsSchema revision.

Thanks!

joncison commented 4 years ago

@matuskalas @hmenager ... me and @hansioan are going ahead with biotoolsSchema 3.3.0 - so if you have suggestions for above, they can be included in a subsequent release.

hechth commented 2 days ago

@joncison @hmenager @matuskalas @hansioan So what's the current status on this? Just came across that and it doesn't seem like this problem is actually solved. Also, there are multiple layers to it - one is how to represent the Galaxy tool(s) for a package and the other is the availability of the tool on a specific server.

hechth commented 2 days ago

@hechth for self reference