Adding OMIA related information to MONDO

[ImkeTammen]

Dear Sabrina and Nico

I have created a form to facilitate submission of OMIA data to Mondo.

Google Sheet https://docs.google.com/spreadsheets/d/1L3wnp83F-YCKUpBMVBVv1fjHqU0Rw1g58AjvpE24owA/edit#gid=0

I propose to start with those diseases in OMIA that have a same/similar disease listed in OMIM - where both diseases are caused by mutations in orthologous genes.

Any feedback on the form - in the google sheet or via zoom would be much appreciated.

Imke

[ImkeTammen]

Based on discussions in meeting on the 2/12/2022 I have updated the mapping file - see version 2 in:

https://docs.google.com/spreadsheets/d/1L3wnp83F-YCKUpBMVBVv1fjHqU0Rw1g58AjvpE24owA/edit#gid=2111247295

I presented information for two disease in OMIA - can I get some feedback that this is what you had in mind for parent / child? I added other columns as discussed and created one line for each 'parent' (OMIA phene entry) and one line for each OMIA phene-species entry)

[katiermullen]

Question from @ImkeTammen: I had a bit more of a look at phene-species in regard to characterisation of ‘defect’. There are about 200 entries that are currently listed as ‘unknown’ and I just wanted to check if they should be yes/no.

In this group there are a range of entries relating to animal models of human disease that have been created via genome editing or other forms of genetic modifications. As they are not a ‘naturally’ occurring disease we have sometimes (butnot consistently) listed them as unknown in regards to ‘defect’. Would you want genome edited/transgenic animals listed in MONDO? If yes than I will add a ‘defect – yes’ classification.

No, we do not want them in Mondo because they are not naturally occurring diseases.

Question from @ImkeTammen: Another group of entries currently listed as ‘unknown’ relate to confirmed or suspected disease ‘resistance/susceptibility’ e.g. ‘Spongiform encephalopathy, susceptibility/resistance to’ or ‘Resistance/susceptibility to lentivirus’ – clearly a quantitative trait – not sure if they should be listed as defect. Resistance to a pathogen is not a defect – susceptibility is. Again would this be something that MONDO would want to include?

Please tag the "disease susceptibility" entries in OMIA because we may want to add them later as there is a human disease susceptibility branch in Mondo.

[ImkeTammen]

We will have to create a new field in OMIA to easily classify genetically engineered / genome edited entries. I will discuss this with Frank and Marius and update you.

I will discuss with Frank how to tag the 'disease susceptibility/resistance' - probably need to rename the field in OMIA to 'disease related' instead of 'defect'

[katiermullen]

@ImkeTammen: I am working on adding the OMIA disease terms to Mondo. @sabrinatoro brought up the follow question which I am hoping you can help me resolve. There is the recurring question about "how was it decided that a non-human disease is analogous to a human disease defined by the gene affected?". Is this because of the orthologous gene?

For example:

For OMIA:002145 what is the logic for this cross-species analog? It is because it is colorectal cancer that is due to the orthologous gene of MLH1 gene?

Same question for OMIA:002241, OMIA:001594, OMIA:001820, OMIA:002032, OMIA:002072

[ImkeTammen]

Dear Katie, I will try and answer tomorrow- just on the way to the airport…

Get Outlook for iOShttps://aka.ms/o0ukef

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From: katiermullen @.> Sent: Tuesday, July 25, 2023 12:55:25 PM To: monarch-initiative/mondo @.> Cc: Imke Tammen @.>; Mention @.> Subject: Re: [monarch-initiative/mondo] Adding OMIA related information to MONDO (Issue #5585)

@ImkeTammenhttps://github.com/ImkeTammen: I am working on adding the OMIA disease terms to Mondo. @sabrinatorohttps://github.com/sabrinatoro brought up the follow question which I am hoping you can help me resolve. There is the recurring question about "how was it decided that a non-human disease is analogous to a human disease defined by the gene affected?". Is this because of the orthologous gene?

For example:

For OMIA:002145 what is the logic for this cross-species analog? It is because it is colorectal cancer that is due to the orthologous gene of MLH1 gene?

Same question for OMIA:002241, OMIA:001594, OMIA:001820, OMIA:002032, OMIA:002072

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[katiermullen]

Thank you, @ImkeTammen. It is not a rush.