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Mondo Disease Ontology
http://obofoundry.org/ontology/mondo
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disease susceptibility should not be a subclass of the disease #2334

Closed nicolevasilevsky closed 3 years ago

nicolevasilevsky commented 3 years ago

@matentzn please do a SPARQL query to find all susceptibility of classes and remove superclass assertions to the the parent disease. For example:

MONDO:0012863 attention deficit-hyperactivity disorder, susceptibility to, 6 should not be a child of MONDO:0007743 attention deficit-hyperactivity disorder

cc @cmungall

maglott commented 3 years ago

How should susceptibilities be treated? Are they phenotypes and not disorders?

nicolevasilevsky commented 3 years ago

Good question @maglott, I think that is a bigger question. @pnrobinson opened this ticket (https://github.com/monarch-initiative/mondo/issues/496) a while ago suggesting we obsolete susceptibility terms.

For now, I think we'll move these OMIM susceptibility terms to children of Mendelian disease.

cmungall commented 3 years ago

I think you mean outside of Mendelian?

yes the susceptibilities should be outside the main hierarchy

On Thu, Nov 19, 2020 at 12:03 PM Nicole Vasilevsky notifications@github.com wrote:

Good question @maglott https://github.com/maglott, I think that is a bigger question. @pnrobinson https://github.com/pnrobinson opened this ticket (#496 https://github.com/monarch-initiative/mondo/issues/496) a while ago suggesting we obsolete susceptibility terms.

For now, I think we'll move these OMIM susceptibility terms to children of Mendelian disease.

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nicolevasilevsky commented 3 years ago

right now, these OMIM terms are classified as Mendelian diseases too (such as 'attention deficit-hyperactivity disorder, susceptibility to, 6' is a child of Mendelian disease and 'attention deficit-hyperactivity disorder'.

I guess they should be asserted to be children of MONDO_0020573 'inherited disease susceptibility', yes?

cmungall commented 3 years ago

yes

we'll work towards making disease susceptibility and disease disjoint... incremental progress

On Thu, Nov 19, 2020 at 4:44 PM Nicole Vasilevsky notifications@github.com wrote:

right now, these OMIM terms are classified as Mendelian diseases too (such as 'attention deficit-hyperactivity disorder, susceptibility to, 6' is a child of Mendelian disease and 'attention deficit-hyperactivity disorder'.

I guess they should be asserted to be children of MONDO_0020573 'inherited disease susceptibility', yes?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/monarch-initiative/mondo/issues/2334#issuecomment-730728151, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMONVFSY4K22UGLOCHBDSQW3YPANCNFSM4T3X5LIA .

pnrobinson commented 3 years ago

@cmungall Please do not do this. There is no disease called X susceptibility. The disease is simply "X". Once can only infer "X susceptibility if one figures out that say Y% people with a mutation in some gene have the disease where Y% is higher than in people without a mutation in the gene. But people with the mutation either have or do not have the disease. @ahamosh could we set up a call to discuss how MONDO should name the diseases where OMIM has X susceptibility? It would be good to agree upon and document our rules.

maglott commented 3 years ago

ClinVar has been inconsistent with this, and would appreciate consensus on a way to go forward. When variants contribute to susceptibility to disorder D, we have curated some to be an interpretation of susceptibility to disorder D, removing the record for "susceptibility to disorder D". But we don't have enough curation resources to maintain all these, and thus have let most be retained as phenotypes given that they are assigned IDs by OMIM, UMLS, and now Mondo.

ahamosh commented 3 years ago

This definitely requires a conversation. Some "susceptibility to" are for germline increased risk that requires additional factors (genetic or environmental), for example: BRCA1 or BRCA2 and Breast and Ovarian Cancer. Having the variant doesn't give you the disease, you need to accumulate more somatic mutations, but it significantly increases the risk. Also UNC93B and HSV encephalitis: if you aren't exposed to HSV young, you won't get the encephalitis. We won't be eliminating those.

Let's set up a zoom to discuss. Please not next week.

nicolevasilevsky commented 3 years ago

@ahamosh we have weekly meetings scheduled on Fridays at 9am PT/12pm ET - are you available then? The meeting is canceled next week due to TG. If that doesn't work, we can find another time. Thanks!

ahamosh commented 3 years ago

Hi Nicole, I have to run a clinical faculty meeting at 9 am on 12/4, but I can do 12/11 barring a patient emergency because I will be on call. Can I have Joanna join?

nicolevasilevsky commented 3 years ago

Hi @ahamosh - great, I'll send you and Joanna an appointment - we'd love to have Joanna join!

nicolevasilevsky commented 3 years ago
nicolevasilevsky commented 3 years ago

moved to a discussion: https://github.com/monarch-initiative/mondo/discussions/2672