obsolete occurent[sic] part-of

[cmungall]

On RO call discussing https://oborel.github.io/obo-relations/process-relations/

proposed to obsolete RO:0002012 occurent part of

currently unused, and if it is used e.g. in logical defs it will lead to cryptic lack of entailments unless complex rolification axioms used

[nlharris]

Note that PR #517 fixed the misspelling (occurent -> occurrent) in RO_0002012

[StroemPhi]

As outcome of discussing this in the context of #486, I propose that when/if this relation gets obsoleted the obsoletion reason annotation should include a link to https://oborel.github.io/obo-relations/process-relations/ for the theoretical background and maybe some analysis code (reference to Uberon?) in which it was checked that the relation is really not used in any axioms of other ontologies but only imported. Which do the latter can be seen in OLS' also in feature. Maybe also an annotation that tells user about the possibility to use the BFO2020 equivalents if such a relation is needed for pure data anotation might be a good idea?

[gouttegd]

I am discovering this discussion just now.

FYI, occurrent part of is currently used as a super property of FBdv’s substage of, which is itself used to express the fact that a developmental stage is a subdivision of another, “larger” development stage (e.g., 'third instar larval stage' substage of some 'larval stage').

The rationale for the creation of substage of in FBdv was, “a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during in RO“. I suppose now that this is never going to happen?

Do I understand correctly that the recommended way of expressing that a stage is a “substage” of another is to use the generic part of relation?

[StroemPhi]

Do I understand correctly that the recommended way of expressing that a stage is a “substage” of another is to use the generic part of relation?

That's at least how I interpret what's stated in https://oborel.github.io/obo-relations/process-relations/:

RO also provides more specific relations: RO:0002012 occurrent part of However, be very careful using these, they are in some sense incompatible with the generic relations. This is because in OWL it is difficult to "infer downwards" a relation hierarchy. For this reason, we recommend using the generic relation, particularly when expressing logical definitions.

[dosumis]

The problem is that using the generic part_of relationship in this case makes temporal reasoning about the relative timing of stages and substages impossible - as this requires links to other relations used in temporal reasoning that have occurents as domain/range.