obophenotype / obophenotype/uberon

Ensure relationships are complete for new tooth terms

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Description

In #1586 some new terms were added - these are all excellent terms!

however, there are some missing axioms. E.g. in

[Term]
id: UBERON:7500059
name: upper third secondary premolar tooth
def: "The premolar tooth of the upper jaw that is phylogenetically number 3." [https://orcid.org/0000-0003-2699-3066]
synonym: "P3" RELATED []
synonym: "upper third permanent premolar tooth" EXACT []
is_a: UBERON:0016944 ! upper premolar tooth
is_a: UBERON:0017270 ! secondary premolar tooth
created_by: https://orcid.org/0000-0003-2699-3066

I believe there should be a link to

[Term]
id: UBERON:7500056
name: premolar 3
def: "The premolar tooth of the upper or lower jaw that is phylogenetically number 3." [https://orcid.org/0000-0003-2699-3066]
synonym: "premolar tooth 3" EXACT []
synonym: "third premolar tooth" EXACT []
is_a: UBERON:0007120 ! premolar tooth
created_by: https://orcid.org/0000-0003-2699-3066

even better is if there is a logical definition. We'd expect logical definitions for all compositional terms. @nicolevasilevsky can we add yaml templates for teeth?

{upper, lower} {primary,secondary} {tooth}

with owl def:

{tooth} and part-of some {upper,lower} jaw region and part-of some {primary,secondary} dentition

@megbalk would you be able to make another PR adding these logical defs, as you are the expert here? Many thanks!

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the new tooth terms from #1586, especially UBERON:7500059 and UBERON:7500056, and compare their existing is_a relationships with the requested links. Then examine how compositional terms and logical definitions are represented in the ontology. Done means the relevant upper/lower and primary/secondary tooth terms have complete relationships and the requested logical definitions or templates.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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