[Revise subclass] DNA repair disorders

[ValWood]

Mondo term (ID and Label)

follow on from https://github.com/monarch-initiative/mondo/issues/3193

Suggested revision and reasons

also these :

ataxia and polyneuropathy, adult-onset (MONDO:0010781) PCNA-related progressive neurodegenerative photosensitivy syndrome (MONDO:0014399 spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 (MONDO:0011801) spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (MONDO:0018996)

I noticed this because I know that a lot of DNA repair disorders cause defects with ~neurogenesis~ neurodegenerative diseases, but my overlap was very small. I checked all the DNA repair disorders annotated at PomBase. There may be others... (although I think the majority DNA repair genes are conserved)

[nicolevasilevsky]

@ValWood are you requesting that these terms be children of DNA repair 'DNA repair disease'?

These three are descendants of 'DNA repair disease' already: PCNA-related progressive neurodegenerative photosensitivy syndrome (MONDO:0014399 spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 (MONDO:0011801) spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (MONDO:0018996)

• [x] @kallia-p could you please add the subClass Of axiom to 'ataxia and polyneuropathy, adult-onset': 'disease caused by disruption of' some 'DNA repair' the source should be: https://orcid.org/0000-0001-6330-7526 and this ticket: https://github.com/monarch-initiative/mondo/issues/3195

Then this class will be inferred as a child of DNA repair disease Thank you!

[ValWood]

These should all be also neurodegenerative diseases

[nicolevasilevsky]

Got it, thanks @ValWood. @kallia-p FYI, these additional changes below should be reviewed before we take any action. If you could please just do the step above with the checkbox, that would be great, and we can come back to these other action items later.

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@ValWood This class is a descendant of neurodegenerative disease:

• 'ataxia-telangiectasia-like disorder 2' (MONDO:0014399)

@ValWood My understanding is polyneuropathy is a disease of the peripheral nervous system (it is classified in Mondo as such), and neurodegenerative disease is classified as a child of 'central nervous system disease' in Mondo.

I wonder if we should reclassify 'neurodegenerative disease' as a child of 'nervous system disorder'? Can there be peripheral neurodegenerative diseases? Our Mondo term has a synonym central nervous system degenerative disorder (which xrefs NCIT here).

• [x] I think we need a new grouping class: 'neurodegenerative disease'

• [ ] we should rename 'neurodegenerative disease' to 'central nervous system neurodegenerative disease', and it should be a subclass of 'neurodegenerative disease.

• [ ] add the parent 'neurodegenerative disease' to 'ataxia and polyneuropathy, adult-onset' (MONDO:0010781)

• [ ] MONDO_0100308 'atatic disorder' should be a child of 'neurodegenerative disease' (see article, this says "Ataxia is a degenerative disease of the nervous system." Then this would make these terms children of 'neurodegenerative disease':

• spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1 (MONDO:0011801)

• spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (MONDO:0018996)

@pnrobinson does this sound okay to you?

[sabrinatoro]

Hello @ValWood I recently joined the Mondo team. We will address your issue as soon as possible. Thank you for your patience. If this is a high priority, please let me know and we can prioritize it. Thank you!

[nicolevasilevsky]

@pnrobinson when you have a chance, could you look at the questions above, thank you! ⬆️ 👀

[nicolevasilevsky]

@pnrobinson and @ahamosh could you look at the comment here and let me know if you agree with the proposed action items: https://github.com/monarch-initiative/mondo/issues/3195#issuecomment-870061610

[pnrobinson]

It is not true that neurodegenerative disease is always CNS (https://pubmed.ncbi.nlm.nih.gov/31008845/):

Peripheral neuropathy is the most common neurodegenerative disease affecting 
hundreds of millions of patients worldwide and is an important cause of chronic pain.

I think this is complicated enough that we should discuss it via zoom rather than in GitHub issues!

[ahamosh]

I agree this needs an intensive discussion in vivo or in vitro.

[ahamosh]

in vitro (zoom), not Github.

[nicolevasilevsky]

per https://github.com/monarch-initiative/mondo/issues/5666, Ada said 'ataxia and polyneuropathy, adult-onset' should not be a child of DNA repair disease

[nicolevasilevsky]

@sabrinatoro reassigning this to you