Potential relabelling of 'processed material'/'processed material entity'

[sebastianduesing]

At the 2024 COB workshop, it was raised that there is some dissatisfaction with the label of "processed material" (aka "processed material entity" in COB) among the non-OBI-developer community. There was no consensus reached about which label was preferred; some of the proposed labels included "constructed material entity", "artifact", and various permutations involving "manufactured", "designed", etc. Opening this issue as a venue to continue this conversation.

[cmungall]

The definition is:

• Is a material entity that is created or changed during material processing

so let's roll up to material processing:

• A planned process which results in physical changes in a specified input material

The label "material processing" would lead most people to believe this is for processes that change the properties of bulk materials (but you should survey more generally). The definition seems more general (I assume "material" should be read as "material entity"). I think the intent is to have a high level separation between processes that operate on physical things vs processes that operate on data or information.

However, I get further confused when I look at the logical definition

achieves_planned_objective some 'material transformation objective'

where the referenced class has a definition:

an objective specifiction[sic] that creates an specific output object from input materials.

The reader is left wondering if the inconsistent wording between the process and the cognate objective is a mistake and the two are misaligned, or if it's just a different way of saying the same thing, or if there is a certain amount of word salad. Is the fact that "specific" is is in one and not the other relevant? One has a plural input and the other singular? One mentions output the other doesn't? The output is referenced to as an object? transformation vs processing?

Most people ignore all these words and look at what has been placed under the class to try and infer the intent. Some example subclasses of 'material processing':

OBI:0000457 ! manufacturing
OBI:0001149 ! gene knock in
OBI:0000712 ! pathogen challenge
OBI:0003555 ! vaginal administration
OBI:0600052 ! dialysis
OBI:0302884 ! extraction
OBI:0600040 ! synthesis
OBI:0000426 ! injection
OBI:0302897 ! asphyxiation
OBI:0302895 ! electrocution
OBI:0000105 ! transplantation
OBI:1110095 ! blood harvesting

As an aside, as ontologists we are trained to ignore labels, but I think placing a lot of these under a label "material processing" will raise eyebrows with non-ontologists.

Some examples of classes not placed under material processing:

OGMS:0000090 ! treatment
OBI:0000694 ! animal feeding
OBI:0000818 ! calibration
OBI:0001953 ! freezing
OBI:0003653 ! fasting
OBI:0600009 ! exposure of material to environment
OBI:0000659 ! specimen collection process

Perhaps there is a reason why "freezing" is not under material processing yet "vaginal administration" is; or why 'blood harvesting' is in it and 'specimen collection process' is not. We could make a table of each of these and see whether they conform to the label, text definition, logical definition + referenced definition, or implied intent. I suspect there would be a lot of intra and inter annotator disagreement and lots of different readings of the same word in the definitions.

And going back to processed material, a material entity that is created or changed during material processing, if asphyxiation is material processing, what is the processed material? (it has to have one, by OBI's axioms). The asphyxiated organism? Are all humans processed materials by virtue of undergoing some kind of nebulous material processing during their life time?

I realize this is easy to criticize and this is all hard because OBI set itself some hard objectives some time ago in how it went about defining things, but I think things need to be made simpler and more intuitive before including in COB, and some of the original constraints in how things were defined can be relaxed.

I think the intent here is to break up planned process into broad categories depending on whether the process involved physical objects and materials, information (as either inputs or outputs), or were more social in nature? That seems like a reasonable user-friendly way to group things. Perhaps start with classes, definitions, and labels that reflect that intent?

[DanBerrios]

Consider an editor's notes entry to try to relate construction and processed material, at least loosely....