Re-engineering Request Death

[johnbeve]

IDOBRU includes a subclass of process that is death. This seems to have been imported from The Gene Ontology.

First thing, the term has been deprecated and replaced by more specific classes, such as cell death. Second thing, there is some ambiguity (not any fault of IDOBRU) over the use of the term. In BFO, there is a sibling class of process called process boundary identifying boundaries of processes having no proper temporal parts. Occurrents like birth and death are considered examples of such markers. This is to say even classes like cell death might plausibly be understood as subclasses of process boundary rather than process. Third thing, to capture relevant occurrents that have proper temporal, parts IDO uses process classes like process resulting in death, which is a process that is marked by a death process boundary.

[linikujp]

We will put death as a subclass of process boundary.

[linikujp]

@johnbeve is there a relation to hold between the date of death with the death (process boundary)? CCO uses occurs on for a process and a temporal region. I think we could adopt that. https://www.nist.gov/system/files/documents/2019/05/30/nist-ai-rfi-cubrc_inc_004.pdf

[johnbeve]

In BFO 2.0 there is a relation occupies temporal region which holds between processes or process boundaries and temporal regions, which we can use.

I'm not able to find the relation occurs on used by CCO in BFO 2.0. They may not have adjusted with the second version updates. The nearby relation occurs in - in BFO 2.0 - holds between a process and a material or immaterial entity.

[linikujp]

@johnbeve I want to make a distinction that occurs on has the range "temporal region", and occurs at has the range "location". And occurs in may take care of the rest?

[johnbeve]

@linikujp I worry CCO using occurs at and occurs on as you've citing is based on terms from BFO that have changed since the CCO document was written (the authors were aware a change might happen to the terms; they say in the document "As of now, BFO..." before introducing occurs on, etc..).

BFO 2.0 has the resources you're looking for though: occupies temporal region has temporal region range and the relation located in has domain and range independent continuants (excluding spatial regions). You can say a death process has a death process boundary as proper part and that boundary occupies some 0 dimensional temporal region. Similarly, you can say a bacteria is located in some a human, cell, etc.

[linikujp]

Agree that occupies temporal region will satisfy the occurs on. relation found in BFO 2.0 file : https://raw.githubusercontent.com/BFO-ontology/BFO/releases/2014-05-03/owl-group/bfo.owl

located in dosen't satisfy the requirement. The domain of "located in" is an "independent continuant". We need the domain to be process and a location. Maybe we could use occurs in: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001]

Things I wanted to cover include the recent CIDO diagnosis modeling the PCR IVD assay being authorized EUA use at a specific facility only (highlighted):

[linikujp]

But the problem is I only want to capture the spatial region but not the spatiotemporal region, unless the spatiotemporal region means something else.

Note that authorized use will have a temporal part related with it.

[johnbeve]

I wanted to reach out and say I've not forgotten about this question; I'm still thinking it through. I've two quick comments though:

The term spatial region is in BFO to identify physical reference frames of the sort you'd find in physics, and isn't often used to characterize what I believe you're after here. More often the term site is used. Sites are on the occurrent side and are distinct from spatiotemporal region, though they can be associated with temporal regions like any other continuant.

I'd also want to keep clear in your diagram above that assays are planned processes in OBI, which are occurrents. They have plan specifications though, which are continuants concretized in those processes. So as I understand the New Haven assay has a plan specification component, which may be concretized in a planned process that would have participants individuals affiliated with Yale New Haven hospital, i.e. individuals who had certain roles in that context.

I'll see if I can spell this out clearer in a bit.

[linikujp]

To clarify the concept, it is more about the entity (authorized organization) who is authorized to run the test at their facility. In this case, the organization only have one facility - the clinical virology lab of Yale New Haven Hospital. However, the authorization is granted to the legal entity Yale New Have Hospital on the EUA authorization letter.