Add process profile to OBO-core

[wdduncan]

Add class process profile to OBO-core ontology, specified as follows:

elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])

[cmungall]

Does obo core need this? What core classes would be subclasses?

On Tue, Dec 3, 2019, 22:15 Bill Duncan notifications@github.com wrote:

Add class process profile to OBO-core ontology, specified as follows:

elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])

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[jamesaoverton]

EDIT: I said 'planned process' throughout but I meant 'process profile'. I update this comment to be sane. Sorry!

A bit of context: On the OBO Operations call yesterday, Barry said that 'process profile' is not included in BFO ISO aka "BFO 2020". He asked if it might have a home in OBO Core. Bjoern told him to make a tracker item to discuss that.

On the call Alan suggested that 'process profile' could live in some branch of BFO. Barry didn't like that idea, but I'm not sure why. My opinion is that the term would be better in BFO somewhere.

[cmungall]

I definitely think planned process needs to be outside BFO and OBO Core is a good home

But this ticket is about process profile?

[jamesaoverton]

@cmungall Yes, that was a complete mental lapse on my part. I've updated my comment.

[hoganwr]

Just curious: Does OBO Core have a namespace? Is it adding things or just bringing things from elsewhere together?

[jamesaoverton]

@hoganwr OBO Core will have its own namespace, and at least some new terms in that namespace.

[cmungall]

Let's go ahead and register it!

On Thu, Dec 5, 2019 at 1:55 PM James A. Overton notifications@github.com wrote:

@hoganwr https://github.com/hoganwr OBO Core will have its own namespace, and at least some new terms in that namespace.

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[bpeters42]

What namespace? OBOC?

On Tue, Dec 10, 2019 at 2:24 PM Chris Mungall notifications@github.com wrote:

Let's go ahead and register it!

On Thu, Dec 5, 2019 at 1:55 PM James A. Overton notifications@github.com wrote:

@hoganwr https://github.com/hoganwr OBO Core will have its own namespace, and at least some new terms in that namespace.

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[cmungall]

Made a new ticket for deciding namespace #54

[cmungall]

Let's go back to the original question. Should process profile be in COB?

I propose the answer is no. COB shouldn't be a place for things rejected from BFO. COB should include only classes that have names and extents meaningful to a domain scientist.

There may be subclasses of process profiles that belong in COB. @wdduncan can you propose some?

[wdduncan]

The Molecular Process Ontology has a few use cases: Baldwin-favoured profile: http://purl.obolibrary.org/obo/MOP_0000773 Baldwin-disfavoured profile: http://purl.obolibrary.org/obo/MOP_0000774

In the Mental Functioning Ontology consciousness ( http://purl.obolibrary.org/obo/MF_000001 is a process profile (along with its subclasses) (interesting ... but foregoing comments).

In OGMS, there were discussions of representing the acute onset of a disease as a process profile.

The request (as noted above) was put in on behalf of Barry. I think we need something that is like process profiles even if don't explicitly add the class. I thought the latest work on "characterizes" relation was meant to address this.

Other potential use cases:

• the rate at which a drug is administered (or the rate of metabolizing a substance)
• the period of cycles within the circadian rhythm
• vital signs: heart rate, breathing rate, change in blood pressure etc.
• how fast a virus spreads through a population

It is conceivable that all these use cases can be addressed using measurement datums about the respective processes. I find this a little unsatisfying though.

[cmungall]

@colinbatchelor @bpeters42 any comments on the MPO profiles? The text definition doesn't cite any literature source. My instinct is that there are simply properties of a process. No need for process profile in COB

A disease onset is a temporal interval like any other, should be treated just like stages in AOs, no need for philosophical abstractions

[cmungall]

I see where you are coming from now. process profile exists to solve an invented artificial problem, namely that BFO does not allow processes to have qualities.

This is solved by #65, ie having a broad class 'characteristic' that encompasses any kind of property without bringing in impractical philosophical constraints

[wdduncan]

I added a comment to #65.
I don't this is an artificial problem, per se. Rather, it is a consequence of how BFO has been developed.
Actually, I am fine with processes having properties, but then either BFO needs to change or we need to define our own axioms or definitions of top level entities.

[addiehl]

Properties of processes are, by their nature, information content entities and should be treated as such. A heart beating process may have an inherent rate, but that rate can only be expressed as a calculated quantity based on beats per some fiat time measurement.

[bpeters42]

I have never understood what process profiles are. I don't understand the MPO examples either. I do understand wanting to describe heart beat rates. But once we can assign durations to processes (and process parts) that is also straightforward? I am also still unclear how to assign a duration to a process in BFO; can we settle on that first, in a practical way? Then I think we can easily define things like heartbeat processes with characteristic durations, the inverse of which are rates.

[bpeters42]

Sorry, closed by accident.

[wdduncan]

Sure, the rate at which my heart beats can be calculated, and the calculation expressed as an ICE. But this doesn't mean that my heart rate is an ICE.
I don't want to muddy the philosophical waters here. We've spent a lot of time going back and forth about this. From a pragmatic standpoint, yes we can represent measurements of rates as ICEs.
Does OBO core need more? PATO seems to think so. see the process quality branch:
http://www.ontobee.org/ontology/PATO?iri=http://purl.obolibrary.org/obo/PATO_0001236

Should all the process qualities be represented using ICEs?

[addiehl]

Yup

[wdduncan]

I think a better approach is to relate process process profiles to processes using the has characteristic relation. That way we don't have to deal with redefining things in terms of ICEs.

[cmungall]

@addiehl

Properties of processes are, by their nature, information content entities and should be treated as such. A heart beating process may have an inherent rate, but that rate can only be expressed as a calculated quantity based on beats per some fiat time measurement

This seems bizarre. What do fiats have to do with anything?

So I suppose velocity and acceleration aren't real properties either?

@wdduncan

Sure, the rate at which my heart beats can be calculated, and the calculation expressed as an ICE. But this doesn't mean that my heart rate is an ICE.

exactly!

[addiehl]

I suppose I worded that badly. The only way talk about properties of processes is as information content entities. The very word rate implies a measurement process and a calculation process. The entity in reality is the beating process, and instances of beating processes can be measured and rates calculated.

Obviously, velocity and acceleration are real, and we measure and model them through mathematics and ICEs. This is what science is about.

But this viewpoint is obviously inconvenient. We can choose to talk about the ICEs as if they are "process profiles" and pretend they are some kind of process (though even Barry Smith has stopped promoting 'process profile', so I cannot understand its revival for COB; it doesn't solve any problems), or simply call them qualities of processes, even though such qualities are fundamentally different from the qualities of continuents (or even continents, as my spell checker would have it).

[bpeters42]

Velocity is a rate of change in location relative to a reference frame/observer. How can that be real, but a heart beat rate is not? As I tried to say up front, can't we start "simple" and clearly spell out how to define the duration in time of a process? I am hopeful if that is clear, rates and the like will become clear too.

On Fri, May 8, 2020 at 8:50 AM Alexander Diehl notifications@github.com wrote:

I suppose I worded that badly. The only way talk about properties of processes is as information content entities. The very word rate implies a measurement process and a calculation process. The entity in reality is the beating process, and instances of beating processes can be measured and rates calculated.

Obviously, velocity and acceleration are real, and we measure and model them through mathematics and ICEs. This is what science is about.

But this viewpoint is obviously inconvenient. We can choose to talk about the ICEs as if they are "process profiles" and pretend they are some kind of process (though even Barry Smith has stopped promoting 'process profile', so I cannot understand its revival for COB; it doesn't solve any problems), or simply call them qualities of processes, even though such qualities are fundamentally different from the qualities of continuents (or even continents, as my spell checker would have it).

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[wdduncan]

There has not been any movement on this issues. Should we close?

[wdduncan]

Sorry ... closed by accident.

[ddooley]

Is this closed because of a decision to use process characteristics rather than implement process profiles in COB? Or just that further discussion will occur elsewhere?