tooth pattern

[meghalithic]

I revised the upper and lower tooth pattern to better fit with what @wdduncan and I have discussed.

I also added a dentition tooth pattern. Dentition takes the outputs from the upper and lower tooth pattern and adds dentition.

The reasoning for separating the pattern is to make the patterns cleaner and because the order of naming teeth are dentition then position (upper/lower) then tooth (e.g., primary lower molar tooth), so separating out dentition from the upper/lower pattern makes sense and prevents teeth from being named as just dentition without identifying if they are upper or lower.

[meghalithic]

how do I create an annotation on "has_exact_synonym" to have "synonym_type_property" and "abbreviation"?

[meghalithic]

@rays22 how do I test this?

[wdduncan]

@megbalk Have you run sh run.sh make IMP=false test locally? Does it complete w/o error?

Also, you can run sh run.sh make ../patterns/definitions.owl -B IMP=false to generate your definitions.owl file. See the DOSDP generate: Turning the template tables into OWL axioms section on this page: https://oboacademy.github.io/obook/tutorial/dosdp-odk/

[meghalithic]

@wdduncan I was talking with a mammalogist @helenamachado , and this is how they write out teeth as tooth number dentition position tooth type:
M3 = third upper molar (assume if deciduous not written, then it is secondary)
dp2 = second deciduous lower premolar

Previously, @markengelstad and I had landed on naming the teeth as primary/secondary upper/lower side number tooth type:
M3 = secondary upper third molar
dp2 = primary lower second premolar

Would it make sense to have a dentition pattern first, since often a paleontologist or mammalogist would know if a tooth is deciduous or not, then have an upper and lower pattern builds off of, or does it not matter (i.e., can use either independently)?

We could have exact_synonyms for the different naming orders.

The order of the patterns is important as it determines the order of the naming.

[wdduncan]

@megbalk I'm not sure if it is better to have dentition or position. The FMA used dentition first (e.g. upper first secondary molar tooth. But, I don't know why.

[markengelstad]

There are many ways to do this, but if you want to be able to use a scalable extensible system that can model anything, then you should include , in order: Dentition first (if organism has > 1 set of teeth) : because it’s consistent and logical, I prefer “Primary” and “Secondary” rather than “deciduous” and “permanent”. Followed by arch: Upper and Lower. (I think this makes more sense than maxillary and mandibular for reasons I Cld explain. ) Then morphology/ form : Incisor , canine, premolar, molar and the sequence from the midline. : 1,2,3 or first, second, third Mark Engelstad

…

________________________________ From: Bill Duncan ***@***.***> Sent: Wednesday, January 11, 2023 2:02:42 PM To: obophenotype/uberon ***@***.***> Cc: Mark Engelstad ***@***.***>; Mention ***@***.***> Subject: Re: [obophenotype/uberon] tooth pattern (Issue #2761) @megbalk<https://github.com/megbalk> I'm not sure if it is better to have dentition or position. The FMA used dentition first (e.g. upper first secondary molar tooth<https://ontobee.org/ontology/FMA?iri=http://purl.obolibrary.org/obo/FMA_55811>. But, I don't know why. — Reply to this email directly, view it on GitHub<#2761 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABPR2B3FUZBKKTP2QK25OBDWR4UYFANCNFSM6AAAAAATMOBGTI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[wdduncan]

correction on my comment above

The FMA used dentition first

The FMA seems to be put the arc first (e.g., upper first secondary molar tooth) ... sorry about that.

For animals that regenerate teeth over their lifetime (e.g., sharks) does the primary/secondary distinction make sense to use?

[markengelstad]

Yeah, agreed. for those species that do not have distinctly different sets of teeth/dentition, you wouldn’t need to specify which set. Mark Engelstad

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________________________________ From: Bill Duncan ***@***.***> Sent: Thursday, January 12, 2023 4:29:32 PM To: obophenotype/uberon ***@***.***> Cc: Mark Engelstad ***@***.***>; Mention ***@***.***> Subject: Re: [obophenotype/uberon] tooth pattern (Issue #2761) correction on my comment above The FMA used dentition first The FMA seems to be put the arc first (e.g., upper first secondary molar tooth<https://ontobee.org/ontology/FMA?iri=http://purl.obolibrary.org/obo/FMA_55811>) ... sorry about that. For animals that regenerate teeth over their lifetime (e.g., sharks) does the primary/secondary distinction make sense to use? — Reply to this email directly, view it on GitHub<#2761 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABPR2B7O4BQM5TTB4HDZVSDWSCOWZANCNFSM6AAAAAATMOBGTI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[meghalithic]

ok, so agreed that it should be: dentition, arch, tooth number and type. So, I'll keep the pattern as is: one of upper and lower (arch) and one for dentition based on the outputs from the arch.

[wdduncan]

dentition, arch, tooth number and type

E.g.: upper first secondary molar tooth -> secondary upper first molar tooth

[meghalithic]

I will test my patterns then!

[meghalithic]

I'm getting the following errors but don't see what is wrong. Could I get some help?

[anitacaron]

What is your complete YAML file?

[meghalithic]

@anitacaron what do you mean?

[anitacaron]

@megbalk I need to check the complete pattern configuration file to be able to help. Is there a PR you're working on?

[meghalithic]

@anitacaron I'm working on branch issue-2761

[github-actions]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[wdduncan]

@megbalk Do you want to keep this open?

[meghalithic]

sure, I won't be able to get to it for a bit fyi

[github-actions]

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[ANiknejad]

Hello,

this publication https://pubmed.ncbi.nlm.nih.gov/27872325/ talks about tooth family unit in polyphyodonts, that includes a functional tooth (ft), a replacement tooth (RT) and a dental lamina (dl).

To study dl transcriptome profiles at different stages, we performed RNA-seq on the total extracted RNA. After alignment to the alligator genome (Green et al. 2014), we calculated the reads per kilobase per million reads mapped (RPKM) levels. Hierarchical clustering showed that dl samples collected from the same stage were grouped tightest (Fig. 1C), suggesting that our dissection method was reliable. However, different stages also showed co-clustering: cap-stage and bell-stage samples were grouped together, and bud-stage and RT-bell samples grouped together. These significant expression profile differences with respect to the point of tooth initiation (cap-stage vs. bud-stage) imply that different gene pathways must be activated to start this process. Principal component analysis also showed that samples collected from the same stage wereclustered together (Fig. 1D).

https://trace.ncbi.nlm.nih.gov/Traces/sra?study=SRP080802
SRP080802 reports libraries for both 'dental lamina' and for 'replacement tooth', and 'dental lamina' are all reported such as 'Pre-initiation stage' in SRA metadata, while library names are as detailed as:

• Dental lamina Early Growth stage ---> bud?
• Dental lamina Initiation stage ----> cap?
• Dental lamina Pre-initiation stage ---> bell?

Should for example 'dental lamina bud-stage' be a new class in Uberon?

@markengelstad do you consider here that having a dedicated class for 'replacement tooth' may be useful to make distinction between functional tooth and replacement tooth?
So far, and as far as I can see, there is only UBERON:0007115 deciduous tooth available in UBERON to reflect 'replacement tooth', and its definition is restricted to mammals, means, diphyodonts

Sorry in advance for this long and detailed message, but it is also an opportunity to have this issue still active!

[wdduncan]

The Oral Health and Disease Ontology has classes for various types of prosthetic teeth.

[cmungall]

I don't think prostheses belong in uberon but I like the DP in OHDO, we should adopt more generally for other anatomical parts

Union triad:

1. Function X = X or prosthetic-X
2. Prosthetic-X = Prosthetic part and analog-of some X

This is of course isomorphic to many DPs, e.g SNOMED SEP...

[ANiknejad]

Sorry in advance but I am lost here, not sure the 2 last messages are related to my post, there are none prosthetic tooth in the
complex tooth family unit of polyphyodonts, but functional tooth (ft), a replacement tooth (RT) and a dental lamina (dl), each one involved in natural tooth development stages

OHD:0000206 functional tooth
Definition: A natural, modified or prosthetic tooth

This class does not allow to distinct the ft and the rt during tooth development in polyphyodonts

My concern here regarding the RNAseq libraries I am currently annotating is to have a deciduous tooth available for polyphyodonts, and not restricted to mammals such as UBERON:0007115 deciduous tooth is. I like the synonym: "temporary tooth" EXACT [FMA:55655] for deciduous tooth.

'tooth replacement' sounds common in literature, see https://pubmed.ncbi.nlm.nih.gov/23788284/
Biology of tooth replacement in amniotes (2013)

[wdduncan]

Sorry, I thought 'replacement tooth' referred to things like tooth implants. Sorry for the misunderstanding.

In the OHD, we distinguish between primary and secondary teeth, but, of course, this is human specific. You may need to distinguish between deciduous and non-deciduous teeth.

Perhaps there is a better label for 'replacement tooth', but I can't think of one.