central and lateral incisor tooth

[meghalithic]

changing definition and EQ
issue #2719

see discussion here on 28/11/2022.

[ghost]

Is there a dbxref to support calling this the "second" incisor tooth?

[ghost]

Hi @megbalk, I don't see any edits that would "break" the ontology in this PR, but from a content perspective I recommend seeking a review from someone qualified in this subject matter.

Some of the terms do not have text definitions and the added synonyms do not have dbxrefs to check.

Regarding, "... phylogenetically number #" in the text definitions... after a cursory search online, I could not find an explanation of a phylogenetic numbering system used in this context. This may be due to a lack of domain knowledge, which is why I recommend seeking a review from someone with subject matter expertise.

The annotation property 'tooth number' mentions an ancestral count and a count along the A-P axis. I don't know if the most anterior tooth in a set is always ancestrally the first to appear. Hopefully someone with domain knowledge could help.

See also #557.

In summary, I recommend:

• adding text definitions where they are missing
• adding dbxrefs to support the synonyms
• seeking someone with subject matter expertise in dentition to review the content

If there is a reference that you can share that describes phylogenetically numbering from an anatomical perspective, I'm happy to take a look and do another review.

[meghalithic]

@cmungall @RDruzinsky could I get some help here?

[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

[anitacaron]

#gogoeditdiff

[github-actions]

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/2024-01-02/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/2024-01-02/uberon-simple.owl
• Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

incisor tooth 1 http://purl.obolibrary.org/obo/UBERON_0018551

Removed

• incisor tooth 1 has exact synonym "central incisor"

• incisor tooth 1 label "central incisor tooth"

• incisor tooth 1 SubClassOf in central side of some incisor region of dentition

Added

• incisor tooth 1 label "incisor tooth 1"

• incisor tooth 1 definition "The incisor tooth of the upper or lower jaw that is phylogenetically number 1."

  • database_cross_reference "https://orcid.org/0000-0003-2699-3066"

• incisor tooth 1 has exact synonym "central incisor"

  • has_synonym_type preferred term when talking about an instance of this class in Homo sapiens

• incisor tooth 1 has exact synonym "first incisor tooth"

incisor tooth 2 http://purl.obolibrary.org/obo/UBERON_0018552

Removed

• incisor tooth 2 has exact synonym "lateral incisor"

• incisor tooth 2 label "lateral incisor tooth"

• incisor tooth 2 SubClassOf lateral structure

• incisor tooth 2 SubClassOf in lateral side of some incisor region of dentition

Added

• incisor tooth 2 label "incisor tooth 2"

• incisor tooth 2 has exact synonym "lateral incisor"

  • has_synonym_type preferred term when talking about an instance of this class in Homo sapiens

• incisor tooth 2 definition "The incisor tooth of the upper or lower jaw that is phylogenetically number 2."

  • database_cross_reference "https://orcid.org/0000-0003-2699-3066"

• incisor tooth 2 has exact synonym "second incisor tooth"

lower central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018601

Removed

• lower central incisor tooth SubClassOf incisor tooth 1

Added

• lower central incisor tooth has exact synonym "lower first incisor tooth"

• lower central incisor tooth SubClassOf in central side of some incisor region of dentition

lower central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018568

Added

• lower central secondary incisor tooth has exact synonym "secondary lower first incisor tooth"

lower lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018602

Removed

• lower lateral incisor tooth SubClassOf incisor tooth 2

Added

• lower lateral incisor tooth has exact synonym "lower second incisor tooth"

• lower lateral incisor tooth SubClassOf in lateral side of some incisor region of dentition

• lower lateral incisor tooth SubClassOf lateral structure

lower lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018570

Added

• lower lateral secondary incisor tooth has exact synonym "secondary lower second incisor tooth"

primary central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018553

Removed

• primary central incisor tooth SubClassOf incisor tooth 1

Added

• primary central incisor tooth has exact synonym "primary first incisor tooth"

• primary central incisor tooth SubClassOf in central side of some incisor region of dentition

primary lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018554

Removed

• primary lateral incisor tooth SubClassOf incisor tooth 2

Added

• primary lateral incisor tooth has exact synonym "primary second incisor tooth"

• primary lateral incisor tooth SubClassOf lateral structure

• primary lateral incisor tooth SubClassOf in lateral side of some incisor region of dentition

upper central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018603

Removed

• upper central incisor tooth SubClassOf incisor tooth 1

Added

• upper central incisor tooth has exact synonym "upper first incisor tooth"

• upper central incisor tooth SubClassOf in central side of some incisor region of dentition

upper central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018593

Added

• upper central primary incisor tooth has exact synonym "primary upper first incisor tooth"

upper central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0016454

Added

• upper central secondary incisor tooth has exact synonym "secondary upper first incisor tooth"

upper lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018604

Removed

• upper lateral incisor tooth SubClassOf incisor tooth 2

Added

• upper lateral incisor tooth has exact synonym "upper second incisor tooth"

• upper lateral incisor tooth SubClassOf lateral structure

• upper lateral incisor tooth SubClassOf in lateral side of some incisor region of dentition

upper lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018594

Added

• upper lateral primary incisor tooth has exact synonym "primary upper second incisor tooth"

upper lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0016455

Added

• upper lateral secondary incisor tooth has exact synonym "secondary upper second incisor tooth"

[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:/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

incisor tooth 1 http://purl.obolibrary.org/obo/UBERON_0018551

Removed

• incisor tooth 1 has exact synonym "central incisor"^^string

• incisor tooth 1 label "central incisor tooth"^^string

• incisor tooth 1 EquivalentTo incisor tooth and (in central side of some incisor region of dentition)

Added

• incisor tooth 1 label "incisor tooth 1"^^string

• incisor tooth 1 definition "The incisor tooth of the upper or lower jaw that is phylogenetically number 1."^^string

  • database_cross_reference "https://orcid.org/0000-0003-2699-3066"^^[string](http://www.w3.org/2001/XMLSchema#string)

• incisor tooth 1 has exact synonym "central incisor"^^string

  • has_synonym_type preferred term when talking about an instance of this class in Homo sapiens

• incisor tooth 1 has exact synonym "first incisor tooth"^^string

• incisor tooth 1 SubClassOf incisor tooth

incisor tooth 2 http://purl.obolibrary.org/obo/UBERON_0018552

Removed

• incisor tooth 2 has exact synonym "lateral incisor"^^string

• incisor tooth 2 label "lateral incisor tooth"^^string

• incisor tooth 2 EquivalentTo incisor tooth and (in lateral side of some incisor region of dentition)

Added

• incisor tooth 2 label "incisor tooth 2"^^string

• incisor tooth 2 has exact synonym "lateral incisor"^^string

  • has_synonym_type preferred term when talking about an instance of this class in Homo sapiens

• incisor tooth 2 definition "The incisor tooth of the upper or lower jaw that is phylogenetically number 2."^^string

  • database_cross_reference "https://orcid.org/0000-0003-2699-3066"^^[string](http://www.w3.org/2001/XMLSchema#string)

• incisor tooth 2 has exact synonym "second incisor tooth"^^string

• incisor tooth 2 SubClassOf incisor tooth

lower central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018601

Added

• lower central incisor tooth has exact synonym "lower first incisor tooth"^^string

lower central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018568

Added

• lower central secondary incisor tooth has exact synonym "secondary lower first incisor tooth"^^string

lower lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018602

Added

• lower lateral incisor tooth has exact synonym "lower second incisor tooth"^^string

lower lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018570

Added

• lower lateral secondary incisor tooth has exact synonym "secondary lower second incisor tooth"^^string

primary central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018553

Added

• primary central incisor tooth has exact synonym "primary first incisor tooth"^^string

primary lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018554

Added

• primary lateral incisor tooth has exact synonym "primary second incisor tooth"^^string

upper central incisor tooth http://purl.obolibrary.org/obo/UBERON_0018603

Added

• upper central incisor tooth has exact synonym "upper first incisor tooth"^^string

upper central primary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018593

Added

• upper central primary incisor tooth has exact synonym "primary upper first incisor tooth"^^string

upper central secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0016454

Added

• upper central secondary incisor tooth has exact synonym "secondary upper first incisor tooth"^^string

upper lateral incisor tooth http://purl.obolibrary.org/obo/UBERON_0018604

Added

• upper lateral incisor tooth has exact synonym "upper second incisor tooth"^^string

upper lateral primary incisor tooth http://purl.obolibrary.org/obo/UBERON_0018594

Added

• upper lateral primary incisor tooth has exact synonym "primary upper second incisor tooth"^^string

upper lateral secondary incisor tooth http://purl.obolibrary.org/obo/UBERON_0016455

Added

• upper lateral secondary incisor tooth has exact synonym "secondary upper second incisor tooth"^^string

[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]

@wdduncan could you please review this PR?

[anitacaron]

@wdduncan you can check the nice diff view here

[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.

[wdduncan]

This seems fine to me.