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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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Review children of chromosomal anomaly (MONDO:0019040) #3160

Closed sabrinatoro closed 2 years ago

sabrinatoro commented 3 years ago

The terms under chromosomal anomaly (MONDO:0019040) are organized inconsistently. For example: 'complete trisomy' (duplication of an entire chromosome) and 'partial trisomy' (duplication of part of a chromosome) are in some cases under the same class (e.g., Down Syndrome), and in other cases under different classes ("total autosomal trisomy" and "partial autosomal trisomy/tetrasomy")

Questions: 1) What should be the main subclasses of “chromosomal anomaly”? It looks like there are different concepts:

2) Mosaic versus complete: In addition to these concepts, each of these anomaly “types” could be ‘Mosaic’ (= anomaly found in some of the cells of the organism) or ‘Complete' (= anomaly is in all the cells of the organism) Should the mosaic/complete "version" of the disease be under one general class (e.g. 'mosaic trisomy 21', 'complete trisomy 21' would be subclasses of "trisomy 21"). (I don't know if there is a mosaic and a complete version for all chromosomal anomalies).

sabrinatoro commented 3 years ago

derived from [https://github.com/monarch-initiative/mondo/issues/3128] [https://github.com/monarch-initiative/mondo/issues/3127]

Issue also related to Monochrom

sabrinatoro commented 3 years ago

@cmungall @nicolevasilevsky Here is a proposal regarding the 'chromosomal anomaly' branch of Mondo. https://docs.google.com/document/d/1rDNYMGwvvgujZ4xQEJ79XBoZFOid03BHYIN3rlLALZo/edit?usp=sharing Please give your feedback/thoughts. Thank you!

sabrinatoro commented 3 years ago

@cmungall : Is there any ontology 'rules' with regard to parentage? Should we avoid mixing concepts within a class? Right now, we are not consistent (see classification of 'autosomal anomaly' versus 'gnonosome anomaly')

My 2 main questions are summarized here: 1) should we 'keep concepts separate' within a class (e.g children of 'chromosome number anomaly' be sub-classified only based on chr number, and not on chromosome types) OR should we 'mix' concepts within classes (e.g. children of 'chromosome number anomaly' be subclassified by chromosome type) 2) should 'autosomal anomaly' and 'gonosome anomaly' be classified based on the chromosome# or on the anomaly type?

(please let me know if we need to include anyone else in this discussion) Thank you!

sabrinatoro commented 2 years ago

Except for 2 terms which will be obsoleted in the June release, this project is done. Closing this issue.