nicolevasilevsky
commented
1 year ago hi @taylordm! Sorry for the delayed reply.
Would it be possible to fill out this template with all the new terms needed, and we can do a bulk upload?
Here are more details: https://mondo.readthedocs.io/en/latest/editors-guide/bulk-request/
Need guidance on how to request this system to be supported in MONDO short of trying to list each individual term as a term request (there are many combinations).
Happy to be available for a discussion about this system of notations and how we can support them in MONDO.
I have also posted this to Peter Robinson for HPO consideration.
This is a somewhat complicated but commonly used clinical cardiac malformation reporting system (Von Praagh) that uses a “normal” condition as one of the categorical conditions for each entry in the triplet -- see attached image which comes in from the last paper linked below.
These are just a few examples below listed out of that system, that are already in Kids First.
And it’s unfortunate that lowercase L is used alongside big-I, so user beware.
{A,d,d} visceroatrial situs ambiguous, ventricular D loop, D great artery malposiiton {A,l,d} visceroatrial situs ambiguous, ventricular L loop, D great artery malposiiton {A,l,l} visceroatrial situs ambiguous, ventricular L loop, L great artery malposiiton {A,x,d} visceroatrial situs ambiguous, unknown loop, D great artery malposiiton {I,l,i} visceroatrial situs inversus; ventricular L loop, inversus-normal great arteries. {S,d,A} visceroatrial situs solitus, ventricular D loop, A great artery malposition {S,d,d} visceroatrial situs solitus, ventricular D loop, D great artery malposiiton {S,l,A} visceroatrial situs solitus, ventricular L loop, A great artery malposition {S,l,d} visceroatrial situs solitus, ventricular L loop, D great artery malposiiton {S,l,l} visceroatrial situs solitus, ventricular L loop, L-normal great arteries. {S,x,l} visceroatrial situs solitus, unknown ventricular loop, L-normal great arteries.
Papers that cover this system:
https://www.ahajournals.org/doi/pdf/10.1161/01.CIR.56.2.139
https://thoracickey.com/anatomy-and-classification-of-congenital-heart-disease/
https://web.archive.org/web/20160507120152id_/http://pubs.rsna.org:80/doi/pdf/10.1148/rg.332125086
So in these cases from Kids First, it’s not so clear cut -- as in the first piece of the triplet, they’re using a majority choice as seen in the top section of the image attached.
(to be filled out later!) Preferred term label:
Synonyms
Definition (free text, please give PubMed ID, if applicable, in format PMID:#######)
Parent term (use OLS, or your favorite ontology browser)
Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?
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