obophenotype
Incomplete partition of the cochlea HP:0011373 textual definition and EQ
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
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?
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.
@rays22 can we touch bases about this? Yes. Sorry for my delayed response @pnrobinson. Would you like me to set up a call?
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.
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
There is Incomplete structure (PATO:0005013). I am not sure if that would work.
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.
@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.
so...something like this? 'has part' some ('Incomplete structure' and ('characteristic of' some cochlea) and ('has modifier' some abnormal))
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
I'll create a ticket in uPHENO and we can discuss this at a meeting for specifics.
@rays22 having trouble importing PATO:0005013 into HP to make this happen.