BFO has many advantages, providing a standard for aligning upper
levels across different ontologies, but current usage suffers some issues:

1. classes very abstract and do not correspond to things in any normal domain of science

The labels in BFO are largely invented by philosophers and are not
part of normal scientific vernacular.

This is compounded by the fact that assertion of subClassOf to BFO
classes forces the BFO hierarchy to be prominent in a generic ontology
display. While in theory it is possible to hide this, overall
resources are limited, and we have yet to see this happen in any
single generic ontology browser, never mind ubiquitously.

2. direct subClassOf assertion

The standard methodology for usage of BFO is to directly assert a
subClassOf axiom to a BFO class.

A more modern ontology development strategy is to assert
characteristics and to infer the subClassOf axiom.

A side-effect of this is asserted polyhierarchies. For example,
asserting that a material anatomical entity is material entity and an
anatomical entity.

3. overcommitting

Some ontologies overcommit to very specific classes without knowing
semantics. It would be better for domain ontologies to focus on
stating the characteristics of entities in their domain and for
classification to the most specific BFO class to be inferred.

4. difficulty in mixing and matching

It is difficult to mix and match different UOs without asserting
confusing polyhierarchies (see above).

Proposal

Create a parallel/shadow hierarchy to BFO, representing
characteristics that can be attributed to entities. For example,
rather than a class 'continuant', we would have a characteristic of
'existing in whole at a moment of time'.

Use an object property has-characteristic to connect entities in
our domain to these characteristics. E.g. instead of asserting
SubClassOf continuant, assert SubClassOf has-characteristic some 'existing in whole at a moment in time'.

We defer on the ontological nature of these characteristics for now,
but note that some can be represented using ontologies like PATO,
e.g. 'bearer of some mass' is the defining characteristic/quality of a
material entity (in fact CARO already uses this to avoid asserting MI).

The general design pattern is:

BFOClass EquivalentTo has-characteristic some BFON(BFOClass)

The BFON class can optionally be renamed. E.g.:

• BFON(continuant) rdfs:label 'exists in whole at point in time'
• BFON(material entity) rdfs:label 'has non-zero mass'
• BFON(independent continuant) rdfs:label 'bearer of something'
• BFON(dependent continuant) rdfs:label 'bears something'
• BFON(process) rdfs:label 'has temporal parts'

Logical axioms can be rewritten in terms of BFON, e.g.

 C DisjointWith D => (has-c BFON(D)) DisjointWith (has-c BFON(D))
 R Domain D => R Domain (has-c BFON(D))

Domain ontologies do not need to commit directly to BFO classes
(although they can). They instead commit to characteristics as
required. If BFO is imported, we get classification to the most
specific classes. If BFO is not important, and we instead import BFON
(plus rewritten axioms), we get the same entailment benefits.

The OWL is logically/semantically equivalent, so it could be argued
this is a pointless exercise in deckchair shuffling. However, when it
comes to human usability there is more to an ontology that logical
axioms. Ontology structure and ontology terminology are impactful.

The BFON structure and lexicon has advantages for both human consumers
and producers of ontologies:

1. Consumers:

The ontology top level can be domain entities that are generally
understood by domain scientists. For example, a top level with classes
such as "social entity", "biological entity", "chemical entity", with
sub-levels for organism, gross anatomical structure, biological
process, investigation, etc.

BFO will still be "there" in the form of BFON classes, but these would
structurally and visually form a side-hierarchy rather than being prominent.

2. Producers:

Ontology developers can focus on asserting characteristics (e.g. as
existential axioms) rather than direct is-a assertion of a BFO
category. This is more in line with modern ontology development
following Rector normalization, avoids assertion of MI.