OntologyRelationsMay19MeetingNotes

What is the scope of "All" needs to be addressed taking in to account some ontologies are canonical and others are outside normal. But "Normal" is contentious.

Sort out the case of cell membrane. Historical part of cell is OK. Is it still a cell membrane?

Two buckets more complex "relation" like expressions that are good for "user interface" versus simpler smaller set of core relations from which we can construct them. No assumption that everything that looks like a relation, is a relation in the sense of RO

On_the_surface_of lake, cell membrane - great if they were the same relation.

The scope of RO is both type level relations and instance level relations. But we make clear which are which.

Same or different identifiers for class/instance relations such as part_of?

Numeric ids for RO terms?

RO commits to BFO as upper level ontology

RO will have separate identifiers for class level and instance level relations. (And different class level ids where the quantification is different).

We will use numerical ids for RO terms.

Development relations: Questions about "simple" binary versions, versus refoccurent (one per occurrent) versus ternary (more than one refoccurrent)

AI: Larry write up oocyte maturation/follicle generation case motivating more than one refoccurent

AI: Fabian to write up case: begins_to_exist_during 9, ends_existence_during 11. Query: Does it exist during 10?

AI: Barry to offer new and consistent names for the development temporal relations

AI: Organize meeting with spatial relation experts to extend RO

Larry Hunter's example of why a single reference occurrence doesn't work

Here is my example of why a single reference occurrence doesn't work (and we need a ternary relation in order to capture the reference occurrent for a particular temporal relation):

• Oocyte fate determination <before> oocyte maturation [reference occurrent oogenesis]
• oocyte maturation <before> follicle maturation [reference occurrent lifespan]

First, note that oocyte maturation needs to have both reference occurrents in order to be able to assert these two things. These are different in that there are a bunch of oogenesis occurents (so we need the reference occurrent), but they all end before the first follicle maturation (so we need the other reference occurrent).

Incidentally, we should be able to infer Oocyte fate determination <before> follicle maturation on something like the basis that oogenesis <part-of> lifespan.