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See link to Mungall draft paper on temporalized relations [https://github.com/cmungall/trel-crit/raw/master/trc.pdf here].

'''Executive Summary'''

Since their inception, biological ontologies have made use of a core
set of relations such as "part of" and "participates in". These
relations were standardized and given a formal interpretation with the
publication of the "Relations in Biomedical Ontologies paper" by Smith
et al in 2005. Recently there has been a proposal to end support for
these simple relations and replace them with more complex
"temporalized relations", as part of the BFO2 OWL release. Ontology
developers would need to replace existing relations with temporalized
ones if they are to be conformant to BFO. The temporalized forms of
"part of" in the current release are "part of at some times", "part of
at all times", "part of at all times that whole exists". This set may
even be extended to more forms in future releases.

This would be a radical change impacting all ontology developers and
users, requiring complex re-engineering. Normally, such an
unprecedented major change would have to be justified by a major flaw
in the current system of simple non-temporalized relations. We might
expect the flaw to be a major hindrance to ontology development or
usage, and the new solution to work better. We might also expect the
flaw to be described in a peer-reviewed publication.

However, this is not the case. There has been no demand from ontology
developers or their users to make this transition. In fact most
ontology developers have not been consulted. The sole justification
for this radical change lies in a formal technicality, concerning the
difference between the intepretation of relations in the Web Ontology
Language (OWL) and the temporal interpretation provided in the
Relations Ontology paper. Most experienced OWL modelers have been
aware of this misalignment for a number of years, and accept this as a
trade-off that comes with the benefits of using OWL. This trade-off
has yet to cause difficulties for practical ontology development and
use. Ongoing work suggests it may even be possible to find some
satisfactory solution to the technicality whilst preserving existing
relations.

Yet despite this lack of mandate, BFO2 does not include simple
relations and provides temporalized relations in their place.

A number of experienced ontology modelers (including myself) have
voiced serious concerns about the temporalized relations proposal. In
addition I observed that less experienced ontology developers and
users are highly confused by the BFO2 OWL proposal - they did not know
how to migrate to or how to use the new relations, and they did not
understand the underlying motivatation for introducing them in the
first place. It was suggested to me that I collect some my objections
in a document, which is what I have done in "A critique of BFO2 OWL
temporalized relations".

The document provides an overview of the temporalization proposal,
focusing on the part-of relation (although it should be understood
that this is for the sake of brevity, and the proposal affects many
more relations). I describe some of the features of BFO2 OWL that are
widely accepted: the meaning of the BFO2 OWL relations are different
from the interpretations in the 2005 Relations paper; important OWL
characteristics such as transitivity and inverses differ from the
reference form; temporalization leads to an increased number of
relations, and these do not always connect together in intuitive
ways. These are not new findings, but bear highlighting, as many
potential BFO2 adopters were not previously aware of them.

I then provide an evaluation of BFO2 OWL, using examples from
ontologies I work on, including the GO. Again, for reasons of space, I
focus on "part of". I show that the current version of BFO2 OWL cannot
accurately represent the parthood relationship between a nucleus and a
cell without giving up on transitivity, a characteristic that is
obviously essential. I also show that temporalized relations hinder
our abilities to use OWL reasoning to check for certain kinds of
mistakes in ontologies. Finally I demonstrate how the rigidity
constraint imposed by BFO2 OWL means we cannot include certain
classes, such as a pre-migratory neural crest cell, in our ontologies.

I consider this to be sufficient to demonstrate that not only does the
current version of BFO2 OWL force overwhelming complexity onto
ontologies, it simply will not work.

Recent discussions suggest workarounds for some of the problems I have
highlighted. These workarounds involve the introduction of even more
temporalized forms of relations, and the introduction of the concept
of a history. Because these are neither formalized nor in the BFO2 OWL
document, I am unable to give a thorough analysis demonstrating my
concerns with these new proposed extension. However, I include a brief
section describing these new relations.

My conclusions are that the temporalized relations in BFO2 OWL should
not be used. They are far, far too complex, and even if this
complexity could be overcome with significant tool support, they do
not work in the currently published form. My recommendations are that
ontology developers continue to use the simple non-temporalized
relations they are accustomed to using, and that these relations
should be supported so long as they are required by the
community. This approach may not be perfect from a formal theoretical
point of view, but it is essentially the approach that has been used
for the last decade, and has not been documented to cause problems.

Mungall paper - Revision history

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