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Ensure relationships are complete for new tooth terms #1593

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cmungall opened this issue May 7, 2020 · 6 comments
Open

Ensure relationships are complete for new tooth terms #1593

cmungall opened this issue May 7, 2020 · 6 comments

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@cmungall
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cmungall commented May 7, 2020

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!

@ramonawalls
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Thanks, @cmungall. @megbalk, I think the logical definitions make sense.

@ramonawalls
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@cmungall @nicolevasilevsky What is the release cycle for UBERON? Once we have the UBERON IDs, we need to make a pull request to OBA to create corresponding traits.

@nicolevasilevsky
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@cmungall can you answer this question above?

@ramonawalls I don't actually know what the release cycle for Uberon is, hopefully Chris can let you know.

@meghalithic
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@cmungall will do! I think a .yml file would be useful

@meghalithic
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@cmungall I was playing around with making a yml file. Is it possible to have a vars = "strings"?

@meghalithic
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It looks like these have been fixed, is that correct?

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