Make zygote stage part of life cycle only in Metazoa.

[balhoff]

Related to #2349. This fixes an issue with taxon constraints in GO for yeast annotations: https://github.com/geneontology/go-ontology/issues/23012

[balhoff]

Need to discuss before merging this; now I'm wondering if instead this other axiom should become a Metazoa-specific GCI:

'anatomical structure' SubClassOf 'existence ends during or before' some 'death stage'

I previously did that for:

'anatomical structure' and ('in taxon' some Metazoa) SubClassOf 'existence starts during or after' some 'zygote stage'

We need to decide exactly which Uberon terms are pan-life and which are metazoan. Is 'life cycle' general? Is 'anatomical structure' general?

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-06-14/uberon-simple.owl
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-06-14/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

life cycle http://purl.obolibrary.org/obo/UBERON_0000104

Removed

• life cycle SubClassOf starts with some zygote stage

[github-actions[bot]]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
• Version IRI: None
• Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

GCIs

Added

• life cycle and (in taxon some Metazoa) SubClassOf starts with some zygote stage

life cycle http://purl.obolibrary.org/obo/UBERON_0000104

Removed

• life cycle SubClassOf starts with some zygote stage

[github-actions[bot]]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

[cmungall]

@balhoff I think we should go ahead and merge this. This PR is consistent with your sketch of what are the general terms in #2349

I'm actually not sure I am following your comment above. zygote is certainly more specific than the beginning of life. but to make start and end mirror each other maybe there should be a generic "coming into existence stage" with zygote stage a subclass?

In any case let's merge this and continue discussing details on the main issue