Revise pattern to use 'variation instead of 'mutation'

[nicolevasilevsky]

For the disease series by gene pattern, we create terms that are labeled: [disease] caused by mutation in [gene]

We propose to change the primary label to: [disease] caused by variation in [gene]

per @courtneythaxton's advice on https://github.com/monarch-initiative/mondo/issues/3123#issuecomment-893839567

@ahamosh please let us know if there are any objections to using 'variation' in the primary label in place of 'mutation'.

Action items:

• [x] revise pattern to use variation in primary label and add 'disease caused by mutation in gene' as an exact synonym
• [x] search and replace throughout the mondo-edit.obo file to replace usage of mutation with variation for terms that use this pattern.

[ahamosh]

Do you want just variation or do you want pathogenic variant(s), or pathogenic variation? I have no problem with removing the word mutation, but it is much easier to search for and find the word mutation than variant or variation.

[courtneythaxton]

Hmm, you ask a good question @ahamosh. My first instinct would be to suggest just variation, however I understand that use of "variation" would indicate possibly more than one variant that is causative, or pathogenic for the related disease. My only worry with saying pathogenic variant, is whether all of these variants have been evaluated per ACMg guidelines. There will be instances like Sickle Cell Anemia that are well established, however there could be newer gene-disease relationships that show a single variant in multiple (like 5 or less) un-related individuals, but may not have enough alternative data to support a pathogenic classification.

[nicolevasilevsky]

On the Mondo call, we decided to use variant instead of pathologic variant.