Property chains over develops_from

[gouttegd]

This issue is intended to supersede both #784 and #785, as well as obophenotype/uberon#2723. Those issues are interrelated and I believe it would be clearer to discuss them in a single place.

Current state

Uberon currently injects the following two property chains:

(A) 'develops from' o 'part of' SubPropertyOf: 'develops from'

(B) 'part of' o 'develops from' SubPropertyOf: 'develops from'

(Of note, the chains are injected just prior to reasoning, and are then forcibly removed, so that they are not present in any Uberon released artefacts.)

RO also contains the following related chain:

(C) 'has part' o 'develops from' SubPropertyOf: 'has developmental contribution from'

The question is about the correctness and usefulness of chains A and B.

Stated opinions

@balhoff “I still think both chains are incorrect. In any case the chains should be added to RO to not to Uberon.” src

@cmungall “We agreed a year ago [that woud mean around 2022] to get rid of [chain B], no controversy. Let’s make a separate RO issue for adding the rollification constraint on [chain A].” src Which I take to mean, chain B should not exist at all anywhere (not in Uberon, not in RO), and chain A should be in RO where it may optionally be further refined. The “separate RO issue” is #784, which has not been acted upon yet (likely for lack of clarity of the issue’s message).

Attempt at resolution and objection

Since there was apparent agreement (as stated by @cmungall) that chain B should be removed (“no controversy”), a PR to do just that had been submitted to Uberon (obophenotype/uberon#3197), from where it emerged that, in addition to removing the B chain, the C chain (in RO) should be updated to become

(C’) 'has part' o 'has developmental contribution from from' SubPropertyOf: 'has developmental contribution from'

(This is issue #785, which has not yeen been acted upon.)

But then, @dosumis dissented about the removal of chain B: “We are unsure why this property chain is being removed (apart from that it ultimately should come from RO). It is doing useful work for inference that we likely can’t effectively manage by hand.” src At the same time, he proposed that chain A (the chain that @cmungall wanted to keep and move from Uberon to RO) “should be removed -- has_developmental_contribution_from is sufficient`”.

There thus seems to be a fundamental disagreement about the correctness of the A and B chains. The one non-controversial aspect, I suppose, is that, should they be kept, they should belong to RO and not to Uberon (which is why I created this ticket here rather than in Uberon, where the problem originated).

[ddooley]

Nov 4, 2024: @gouttegd, @dosumis and @cmungall, agreed whatever property chain survives this discussion shall be in RO. Any chance you all can make the next Dec. 2 RO call to discuss? Seems the "part of" semantic component needs discussing in the property chain.

[wdduncan]

Per @cmungall: A reasoner diff can help to guide this discussion.
@gouttegd will make a PR to compare the diffs.

Other discussions about PR to take place on Slack and will update next meeting (hopefully).