Add present_in_taxon statements

[balhoff]

Add present_in_taxon statements for male and female external genitalia to ensure they work in both mammals and insects. These terms are used in the AISM ontology; this will ensure that the usage remains valid as the ontology changes.

cc @JCGiron @sergeitarasov

[JCGiron]

I would also edit the definition of external male genitalia to make it clear that "including the penis and scrotum" is just an example and not the whole extent of the usage of this term.

[balhoff]

Thanks @JCGiron, I made a small tweak to the definition.

[cmungall]

This looks good. You should feel free to propose a more significantly altered definition that is less biased to mammals (I am not a fan of the GO-style definitions that say "an example of this is found in <narrow taxon>" when the true applicability is much broader). @balhoff I have some ideas about more powerful present-in axioms that would entail some of these more specific statements

…

On Mon, Jan 15, 2024 at 5:00 PM Jim Balhoff ***@***.***> wrote: Thanks @JCGiron <https://github.com/JCGiron>, I made a small tweak to the definition. — Reply to this email directly, view it on GitHub <#3172 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOLKPJO25GDRQYEU763YOXGLRAVCNFSM6AAAAABBYTLZMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJSHEZDINJXHE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[github-actions]

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

[github-actions]

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

[github-actions]

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

[anitacaron]

#gogoeditdiff

[github-actions]

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

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-06-10/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
• Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-06-10/uberon-base.owl
• Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

external female genitalia http://purl.obolibrary.org/obo/UBERON_0005056

Added

• external female genitalia RO_0002175 NCBITaxon_9606

• external female genitalia RO_0002175 NCBITaxon_50557

external male genitalia http://purl.obolibrary.org/obo/UBERON_0004053

Removed

• external male genitalia IAO_0000115 "The external masculine genital organs, including the penis and scrotum."
  • hasDbXref "MP:0009199"

Added

• external male genitalia RO_0002175 NCBITaxon_9606

• external male genitalia IAO_0000115 "The external masculine genital organs. In mammals, this includes the penis and scrotum."

  • hasDbXref "MP:0009199"

• external male genitalia RO_0002175 NCBITaxon_50557

[github-actions]

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:/__w/uberon/uberon/master/src/ontology/uberon-edit.obo

Right

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

Ontology imports

Ontology annotations

external female genitalia http://purl.obolibrary.org/obo/UBERON_0005056

Added

• external female genitalia present in taxon Homo sapiens

• external female genitalia present in taxon Insecta

external male genitalia http://purl.obolibrary.org/obo/UBERON_0004053

Removed

• external male genitalia definition "The external masculine genital organs, including the penis and scrotum."^^string
  • database_cross_reference "MP:0009199"^^string

Added

• external male genitalia present in taxon Homo sapiens

• external male genitalia definition "The external masculine genital organs. In mammals, this includes the penis and scrotum."^^string

  • database_cross_reference "MP:0009199"^^string

• external male genitalia present in taxon Insecta

[anitacaron]

Hi @balhoff, let me know if you need someone to approve this.

[balhoff]

@anitacaron yes, please!

[aleixpuigb]

Please, see inline suggestions.