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FlyBase / drosophila-developmental-ontology

The home of the Drosophila developmental ontology, an ontology of Drosophila melanogaster developmental stages.
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question about last release of fbdv-full.obo #88

Closed ANiknejad closed 7 months ago

ANiknejad commented 9 months ago

Hello Damien @gouttegd

in https://github.com/FlyBase/drosophila-developmental-ontology/releases/download/v2023-12-07/fbdv-full.obo released '4 days ago', I am wondering about

[Term] id: FBdv:00007022 name: embryonic cycle interphase def: "The interphase (GO:0051325) of an embryonic cycle." [FBC:DOS] is_a: FBdv:00007024 ! biological process is_a: GO:0051329 ! mitotic interphase intersection_of: GO:0051325 ! interphase intersection_of: FBdv:00018001 FBdv:00007011 ! substage of embryonic cycle relationship: FBdv:00018001 FBdv:00007011 ! substage of embryonic cycle

and

[Typedef] id: FBdv:00018001 name: substage of namespace: relationship def: "A relation between a developmental stage and another, larger developmental stage during which it happens." [FBC:DPG] comment: Creating this relation as a temporar> [Typedef] id: FBdv:00018001 name: substage of namespace: relationship def: "A relation between a developmental stage and another, larger developmental stage during which it happens." [FBC:DPG] comment: Creating this relation as a temporary fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO. is_transitive: true is_a: RO:0002012 ! occurrent part of is_a: RO:0002092 ! happens duringy fix, pending adding the axiom occurrent_part_of subproperty of happens_during to RO. is_transitive: true is_a: RO:0002012 ! occurrent part of is_a: RO:0002092 ! happens during

Is there a refinement of the relationships into FBdv scheduled? I am asking because currently in charge of building new developmental ontologies for various arthropods species, I am looking to following as much as possible the FBdv ontology rules.

Many thanks in advance for any explanation. Best regards,

Anne

gouttegd commented 9 months ago

Hello Anne,

Is there a refinement of the relationships into FBdv scheduled?

No. And the “temporary fix” mentioned in FBdv:00018001 (which has been there for quite a while, by the way: it’s not a new thing from the last release) is likely to become a permanent fix, because the OBO Relation Ontology is seemingly no longer considering making occurrent_part_of a subproperty of happens_during. In fact, they are considering obsoleting occurent_part_of (https://github.com/oborel/obo-relations/issues/518), and to promote the use of part_of instead to express temporal partonomy relationships – something that we can’t do in FBdv because we use those relationships in DPO to automatically classify lethal phenotypes.

ANiknejad commented 9 months ago

Thank you very much for your explanations, Damien!

Clare72 commented 7 months ago

closing this as nothing further to do