NTR 'measurement method of' (previously in AgrO)

[KrishnaTO]

Hello, I'd like to request adding measurement method of to RO along with the following details:

Label: measurement method of Definition: A relation between a plan specification and a 'specifically dependent continuant', in which the plan specification groups the specifically dependent continuant(s). Uses: area measurement protocol, material area density mesurement protocol, pivot lenght measurement protocol, etc ORCID: https://orcid.org/0000-0002-8461-9745

Can be a discussion if domains and ranges are needed. plan specification specifically dependent continuant

Originally a question in issue #505

[ddooley]

So this is a shortcut relation for something like "'plan specification' and 'executed by' some (assay and 'has specified input' some 'generically dependent continuant') "?

I think if you are going to label it "measurement method of" then it would be great to reference a measurement process - probably an "assay" in the definition?

[KrishnaTO]

"'plan specification' and 'executed by' some (~~assay~~ 'planned process' and 'has specified input' some 'generically dependent continuant')

'planned process' is sufficient IMO, where assay (subclass of 'planned process') requires some 'objective to produce information' which is just forces a grouping of classes.

definition [v2] - A relation between a 'plan specification' and a 'specifically dependent continuant', in which the 'plan specification' is carried out according to a 'planned process' that outputs a 'specifically dependent continuant'.

By this logic, it would be ideal to setup/use this relation only with a dosdp pattern, so that it forces a use of a 'plan specification' and 'planned process' with a 'specifically dependent continuant'.

[nlharris]

What remains to be done here?

[KrishnaTO]

If there aren't any issues from @ddooley or from one of the other RO experts, I think this term can be moved with the added definition.

In which case, I can make a PR?

[matentzn]

Feel free! RO = community resource :)

[ddooley]

I do find the definition insufficient because it doesn't include the concept/semantics of measurement that the label "measurement method of" states. On what basis are specifically dependent continuants being grouped?

One way to define this better would be to say 'measurement method of' has domain 'measurement protocol'. And then for 'measurement protocol' an axiom 'executed by' some 'measurement process' (although at moment 'executed by' is just a COB relation).

[ddooley]

Can an example be spelled out too: an "area measurement protocol" is a 'measurement method of' some area". Is that right?

[nlharris]

Is this now a change request rather than a new term request?

[cboelling]

I have difficulty understanding the proposed definition. What does "groups the specifically dependent continuant(s)" mean? Can examples be provided that illustrate the intent of the proposed relation?

[ddooley]

In Agro the relation "measurement method of" has a variety of uses:

AgrO I think has an inverse "has method" with two axiomatizations:

I shy from using "method" in label because method is often construed as a process.

Seeing that the domain is of protocol, and the range is characteristic, a full label would be "measurement protocol of characteristic" and its inverse: "characteristic has measurement protocol".

[wdduncan]

@KrishnaTO I am unsure what you mean by

outputs a 'specifically dependent continuant'

in

definition [v2] - A relation between a 'plan specification' and a 'specifically dependent continuant', in which the 'plan specification' is carried out according to a 'planned process' that outputs a 'specifically dependent continuant'.

Your proposed label includes the word 'measurement'. So, you are saying that the output is a measurement datum? If so, the range of the relation would be (concretizes some measurement datum). Or are there outputs other than measurement datums?

[wdduncan]

@KrishnaTO @ddooley
Is there a case in which the measurement protocol/specification is not used during a planned process? If not, this may be an OBI issue. A measurement protocol would be a subtype of OBI's protocol class, and measurement process could be defined as a planned process that has_specified_input some measurement protocol.

Also, RO doesn't include the class plan specification, which also makes me think this is something for OBI.

I'm not a fan of executes b/c it includes the property chain realizes o concretizes (see also: https://github.com/OBOFoundry/COB/issues/217).

[ddooley]

@wdduncan OBI has been asked to critique this term/definition which we did yesterday. I forgot to mention above that this issue is about moving the AgroO relation to RO. The requested relation appears always to attach between a "measurement protocol" and a characteristic. Its a shortcut for having a protocol as part of a plan specification executed by a measurement process that is measuring some characteristic. I think COB would want to take on the "planned process" executes some "plan specification" axiom BECAUSE its in the definition of planned process?! (Also planned processes execute protocols, rather than take them in as input).

I suggest starting from the most wordy version of the relation, and work back from there if smoother language can be accommodated, so, rather than "measurement method of" how about:

label: measurement protocol of characteristic definition: An object property which attaches between a protocol part of a plan specification that is executed by a [measurement] process with the objective of measuring some characteristic of an entity.

I'm not sure we need to create a "measurement process" per se. since there is "assay", (but I see that measurement process is a bit more generic language).

[wdduncan]

Thanks @ddooley

Its a shortcut for having a protocol as part of a plan specification executed by a measurement process that is measuring some characteristic.

Do you have a specific example of usage you can share?

Also, part of what I don't like about the executes relation, is that linguistically we often speak of machines/people/agents executing plans. The process is what happens as a results of the agent carrying out the instructions. But, with the executes relation, it is the process that does the executing, not the agent. Anyway, that is topic for a different issue ...

[KrishnaTO]

I think COB would want to take on the "planned process" executes some "plan specification" axiom BECAUSE its in the definition of planned process?! (Also planned processes execute protocols, rather than take them in as input)

This is also AgrO's intended use, from my perspective (much to my unfortunate attempts to muddle the definitions before).

label: measurement protocol of characteristic

Need to involve @marieALaporte and/or @celineaubert for acceptance of label change into AgrO.

definition: An object property which attaches between a protocol part of a plan specification that is executed by a [measurement] process with the objective of measuring some characteristic of an entity.

I'm not sure we need to create a "measurement process" per se. since there is "assay", (but I see that measurement process is a bit more generic language).

The addition of the intermediate measurement process or the existing assay will require some additional relation updates in AgrO, but if I have it correct, the proposed measurement process will be:

1. Area measurement protocol equivalent to measurement process some area measurement.
2. area measurement equivalent to measurement method of some field area

whereas currently, it is:

1. Area measurement protocol equivalent to measurement method of some field area

[ddooley]

That last 'area measurement protocol' sentence is fine, we'd just be looking at a relabeling of the relation (if one accepts my opinion that method sounds too much like process rather than protocol):

Area measurement protocol equivalent to 'measurement protocol of characteristic' some field area

Lets just assume "assay" for now, not add "measurement process". Though I listed the expansion of the "measurement method of" relation, I don't think AgrO needs to add that expansion to itself. Shortcuts don't necessarily have to be backed up with the expansion representation. Shortcuts are used when the expansion isn't needed.

The "equivalent to" has to have the same kind of entity on both sides, so:

Area measurement protocol equivalent to measurement process some area measurement

can't be right - a protocol is not a process. A protocol is part of a plan specification which is executed by a process like an assay.

[wdduncan]

@KrishnaTO So, far I am only seeing very general examples about how some hypothetical measurement protocol is related to some hypothetical group of characteristics.

It would be great if you had a specific experiment (i.e., use case) that you could provide as an example. This would be a great help (to me at least).

Are saying that the protocol is about some measurement process that measured one or more characteristics. In OWL, it would be something like this:

'measurement protocol' 'is about' some ('measurement process' that 'has input' some characteristic)

Or do you mean the protocol is about the characteristics? For example:

'measurement protocol' 'is about' some (characteristic that 'input of' some 'measurement process')

An example of usage would help make this clear.

[ddooley]

@wdduncan That first screenshot I gave above shows the examples taken directly from AGRO. As I understand it the way you link characteristics to a process is by way of recently introduced "regulates characteristic" rather than 'has input' some characteristic.

The process changes characteristics of an input, rather than taking in characteristics as input directly. So this "[protocol] 'measurement method of' some [characteristic]" just enumerates all the protocols that can measure something. One might argue that the main interest is in enumerating all the processes that can measure some quality (with each process having a plan specification that mentions a protocol). But if one is detailing protocols, and just having general names for the process, I get why this relationship is desired.

[wdduncan]

@ddooley Thanks for pointing me to the AgrO screen shots :)
Sorry, if my previous comment was not clear. Hopefully, this helps ...

Using the mulch thickness example, here is a made-up example about mulch thickness using instances (it would be nice to have a real-world example).

:mulch-thickness#1 a :mulch-thickness
:mulch#1 a :mulch
:mulch-thickness#1 :inheres-in :mulch#1

And another made-up example about about an instance of a mulch thickness protocol:

:mulch-thickness-protocol#1 a :mulch-thickness-protocol

Here is the part I'm seeking clarity about.

I assume that :mulch-thickness-protocol#1 implicitly related to a measurement process, which I will represent as an anonymous individual _:mp. Now how does _:mp relate to :mulch-thickness#1?

Option 1: Using an anonymous measurement datum:

_:mp a :measurement process

# I'm not a fan realizing concretizations (i.e., 'executes'), but substitute that here if it helps your understanding
_:mp :has-participant :mulch-thickness-protocol#1  

_:mp :has-specified-input :mulch#1 
_:mp :has-specified-output _:measurement-datum
_:measurement-datum :is-about :mulch-thickness#1 

Option 2: The protocol is about the measurement process:

_:mp a :measurement process
_:mp :has-specified-input :mulch#1 
:mulch-thickness-protocol#1  :is-about _:mp  # no measurement datum involved here

Option 1 makes more sense to me. But, I might not be understanding the intent of how the protocol relates to the characteristic.

Also, note that the axiom 'mulch thickness' Subclass Of 'has method' some 'mulch thickness measurement protocol' is too strong. It assert that every instance of mulch thickness is related to an instance of mulch thickness measurement protocol. Surely, there are instances of mulch thickness that are not so related.

[wdduncan]

@ddooley

As I understand it the way you link characteristics to a process is by way of recently introduced "regulates characteristic" rather than 'has input' some characteristic.

The regulates characteristic doesn't seem right to me. Not sure what it means for a protocol (or measurement process) to results in the existence of C OR affects the intensity or magnitude of C, where C is a characteristic.

[ddooley]

@wdduncan I like # 1.

Side note, OBI has your ":mp :has-participant :mulch-thickness-protocol" structured as ":mp executes (':plan specification' and 'has part' :mulch-thickness-protocol)"

"regulates characteristic" doesn't apply to measurement processes for domain. I meant that only as an aside about existing way for some processes to "note" the characteristics of materials they change. A heating water process affects the temperature characteristic (of water).

I think the use of having a list of protocols connected to the characteristics they (through measurement processes) generate datums on shows up where one has a choice of how to measure something, e.g.

• thermometer measurement protocol
• cold/warm/hot finger sensation protocol
• thermal imaging protocol ...

[wdduncan]

Side note, OBI has your ":mp :has-participant :mulch-thickness-protocol" structured as ":mp executes (':plan specification' and 'has part' :mulch-thickness-protocol)"

I was not aware that the executes relation had made its way into OBI. I couldn't find it in the 2022-07-11 version. If it is the same as the STATO:executes relation, then it unfortunately (in my opinion) is defined by the property chain realizes o concretizes.

@wdduncan I like # 1.

So do I :)
However, we need a different label than has method. For now, let's call it foo. The definition for foo might go something like this (adapted from IAO is quality measurement of):

x foo y means x is a measurement protocol, y is a characteristic, and there is a measurement process that uses/utilizes x to output a measurement datum that is about y.

How does that sound?

Some possible labels for foo?:

• measurement protocol defines characteristic (or its inverse characteristic defined by measurement protocol)
• defines measurement of characteristic
• specifies measurement of characteristic

What labels do you suggest?

[ddooley]

@wdduncan Oh brother- I overstepped. I forgot "executes" is coming from COB which is as you say coming from STATO.

Yes, your defn. sounds fine!

Names names names. measurement protocol mentions characteristic (in line with existing "mentions" RO relation) measurement protocol about characteristic (info doc is allowed to be about one or more things?) hmm.

[wdduncan]

@ddooley yes names are a pain :(

Does measurement protocol need be in the name, or can we short just protocol? If so (to build of your examples), how about protocol about measurement of characteristic?

Also, if we want domain/range constraints, we would need to protocol and characteristic to RO. Will this be an issue?

[ddooley]

"protocol about measurement of characteristic" sounds fine to me. @KrishnaTO ?

Can't speak for RO, but I'd think given how core the process model is, that they'd be welcome.

[wdduncan]

One last suggestion (hopefully). I think it may be advantageous to generalize the relation to:

• about measurement of characteristic
• domain: generically dependent continuant
• range: characteristic

This still satisfies the use case, but will also allow for other things that may be about the "measurement of characteristic"

[ddooley]

Great!

[wdduncan]

@KrishnaTO @ddooley Please the definition I created for is about measurement of characteristic in PR https://github.com/oborel/obo-relations/pull/655.

x is about measurement of characteristic y means that 
 - x is an information content entity
 - y is a pato:quality (characteristic)
and there is a process that utilizes x to output information that is about y.

Is this what you are wanting?

I also have a very similar term named is characteristic measurement of with definition:

x is characteritic measurement of y means that:
  - x is an information content entity
  - y is a pato:quality (chacteristic)
and x is about the measurement of y.

From what I recall, is characteristic measurement of is not what you were looking for. Right?

[jamesaoverton]

I think I understand the motivation behind this request, and agree that it's important to get it sorted out. I'm working on a proposal to more clearly link characteristics to the processes that measure them: https://github.com/jamesaoverton/qqv. I think that work is relevant to this discussion, or at least would help clarify the intent here.

As an OBI developer, I think that it's more useful to talk about assays (and types of assays) than about protocols. One reason is that we have more than a thousand assay terms defined, and would not like to create a shadow hierarchy of protocols for every assay type.

I'd appreciate some time to make an alternative proposal to address this use case.

[wdduncan]

@jamesaoverton Based on the discussion so far, the request was for relating protocols to characteristics. The intervening process is mentioned in the proposed definition for is about measurement of characteristic.

x is about measurement of characteristic y means that 
 - x is an information content entity
 - y is a pato:quality (characteristic)
and there is a process that utilizes x to output information that is about y.

However, if they prefer to use assays instead, I can close the PR.