Incomplete partition of the cochlea HP:0011373 textual definition and EQ

[anna-anagnostop]

While reviewing MP-HPO logical mappings for decreased cochlear coiling MP:0003148 and Incomplete partition of the cochlea HP:0011373 , both EQs were shown to use:

has part some (decreased coiling and (characteristic of some cochlea) and (has modifier some abnormal))

I am uncertain as to whether the HPO textual definition matches the EQ.

Could you please clarify the textual definition for the HPO term so that I can determine if the logical mapping is correct?

In other words, is the formation of the cochlea partition formed by coiling of the cochlea?

Thanks so much,

Anna

[pnrobinson]

I think the EQ is incorrect. @matentzn @LCCarmody do we have a pattern for the incomplete formation of a partition/septum that is normally there and its partial absence is the abnormality?

[matentzn]

I assigned @rays22 (@pnrobinson @rays22 is our new EQ expert and can be tagged on all EQ related tickets) to respond and help @LCCarmody to determine a solution.

[pnrobinson]

@rays22 can we touch bases about this?

[rays22]

@rays22 can we touch bases about this? Yes. Sorry for my delayed response @pnrobinson. Would you like me to set up a call?

[matentzn]

Is this still relevant?

[LCCarmody]

I have not worked on it. cursory look, the text definition could be expanded, but I don't think the human version of this exactly matches the mouse phenotype. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635626/#:~:text=6%2D%20Incomplete%20Partition%20of%20the,and%20various%20internal%20architecture%20defects.

[pnrobinson]

Coming back to this, I do not think it is a great idea to have the logical definition reflect our presumption about the pathophysiology (coiling). We should create a PATO term for incompletely partitioned and use it for MP and HP. @matentzn @rays22 @LCCarmody

[LCCarmody]

There is Incomplete structure (PATO:0005013). I am not sure if that would work.

[rays22]

I am fine with using either Incomplete structure (PATO:0005013) or a newly created PATO incompletely partitioned quality in the EQ. Let me know if I should create a term request (and a PR) in PATO for incompletely partitioned.

[pnrobinson]

@LCCarmody @rays22 I would favor Incomplete structure because developmental defects like this are extremely complex and it is not going to be possible to model them precisely with OWL.

[LCCarmody]

so...something like this? 'has part' some ('Incomplete structure' and ('characteristic of' some cochlea) and ('has modifier' some abnormal))

[anna-anagnostop]

Yes, but we will need to request a new pattern for ‘incomplete structure’ and discuss where it is appropriate to use it. ZP and XPO already use PATO:0005013 , see otolith incomplete structure, abnormal ZP:0022484 and abnormally incomplete structure of forebrain XPO:0115310

[LCCarmody]

I'll create a ticket in uPHENO and we can discuss this at a meeting for specifics.

[pnrobinson]

@LCCarmody @anna-anagnostop @rays22 can we move forward with this?

[LCCarmody]

@rays22 having trouble importing PATO:0005013 into HP to make this happen.

[LCCarmody]

sorry, cut off too soon. Could you help? thanks.

[rays22]

Hi @LCCarmody , Here is a PR that is intended to import PATO:0005013 incomplete structure into HP.