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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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[Revise subclass] DNA repair disorders #3195

Open ValWood opened 3 years ago

ValWood commented 3 years ago

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 commented 3 years ago

@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)

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

ValWood commented 3 years ago

These should all be also neurodegenerative diseases

nicolevasilevsky commented 3 years ago

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.

@ValWood This class is a descendant of neurodegenerative disease:

@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).

@pnrobinson does this sound okay to you?

sabrinatoro commented 3 years ago

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 commented 3 years ago

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

nicolevasilevsky commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

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

ahamosh commented 3 years ago

in vitro (zoom), not Github.

nicolevasilevsky commented 1 year ago

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 commented 1 year ago

@sabrinatoro reassigning this to you