Does COB want to inherit "system" from RO?

[ddooley]

With reference to https://github.com/oborel/obo-relations/issues/607 we need a decision from COB about taking on "system", which RO seeks to deprecate for lack of modelling support (if there is a group that wants to focus on systems modelling over and beyond process modelling we welcome that!).

Currently the RO definition of system is: A material entity consisting of multiple components that are causally integrated."

After RO obsoletes "system", then ENVO will need a new parent term for "environmental system".

[cmungall]

I vote no on this.

The term "system" is too vague, many different entities have system-like aspects.

If you want to say your class has a system-like aspect then just go ahead and describe what that system-like aspect is, no need for a vague upper ontology term.

I am responsible for adding this to RO, I think this was a mistake. As far as I know the only place it is used is in ENVO, and I don't think it adds any value there:

Other ontologies that refer to systems (e.g anatomical system in uberon, system process in GO) don't actually use the RO class.

[bpeters42]

I agree with Chris. the first systems I am thinking of (systems of differential equations, systems of government) aren't even covered, and the terms currently in ENVO would not seem to suffer when not being grouped together; 'observatory system' seems to be better placed under 'processed material' (or device) anyway.

On Fri, Jul 1, 2022 at 12:46 AM Chris Mungall @.***> wrote:

I vote no on this.

The term "system" is too vague, many different entities have system-like aspects.

If you want to say your class has a system-like aspect then just go ahead and describe what that system-like aspect is, no need for a vague upper ontology term.

I am responsible for adding this to RO, as far as I know the only place it is used is in ENVO, and I don't think it adds any value there:

[image: image] https://user-images.githubusercontent.com/50745/176790679-cdae3d78-41f0-47de-adbe-5d9660f37b9e.png

Other ontologies that refer to systems (e.g anatomical system in uberon, system process in GO) don't actually use the RO class.

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[pbuttigieg]

We'll create and maintain system in ENVO. I don't think it's vague at all.

'observatory system' seems to be better placed under 'processed material' (or device) anyway.

This makes absolutely no sense to me.

[bpeters42]

Hi Pier,

If you think 'system' is not vague, can you point out what material entities are not "A material entity consisting of multiple components that are causally integrated"? Maybe I just fail to understand what 'causally integrated' means. It seems that all devices (microscopes, pipettes, MRI machines) would be systems. So would 'system' would be a parent of devices? But also organisms seem to fall under systems? Cells? Proteins? What about a stack of apples, where the position of each apple is causally dependent on the others?

Regarding 'observatory systems', within OBI those would fall under devices (material entities produced with the intent to have a function) where the function would be to observe something. If that makes no sense to you, can you elaborate a bit?

• Bjoern

On Fri, Aug 12, 2022 at 9:10 AM Pier Luigi Buttigieg < @.***> wrote:

We'll create and maintain system in ENVO. I don't think it's vague at all.

'observatory system' seems to be better placed under 'processed material' (or device) anyway.

This makes absolutely no sense to me.

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[cmungall]

Just picking up this conversation again.

@pbuttigieg

We'll create and maintain system in ENVO. I don't think it's vague at all.

This is not unreasonable as an incremental step - after 10 years no one else has used "system" other than ENVO. So if ENVO needs it to group "carbonate system of ocean water" with "ecosystem" and "processing line" that becomes an ENVO issue, and we can discuss the relative merits of that grouping on the ENVO tracker.

However, there is a possibility we are missing out on a potentially useful grouping that could be used for other ontologies here. @pbuttigieg maybe you can help us understand the use case for grouping this way and help us determine objective criteria for classification that is less vague?

I apologize for using the term "vague" in my original comment - it would be better to say that there needs to be more documentation on how to apply this class consistently.

Also, I will make an issue in the ENVO tracker to adopt "system"

'observatory system' seems to be better placed under 'processed material' (or device) anyway.

This makes absolutely no sense to me.

I think you are right in that the label is confusing. I made an issue for this on the OBI tracker; https://github.com/obi-ontology/obi/issues/1718

But note that "processed material entity" is now in COB. I still think there are some issues with scope of this class but I think this is a side issue here. We can make a new COB issue for this.